11-36573607-G-A

Variant names:

• chr11-36573607-G-A
• rs4151025
• NM_000448.3:c.303G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BA1 BP7 BS2_Supporting

This summary comes from the ClinGen Evidence Repository: The c.303G>A (p.Ala101=) variant (NM_000022.4) is a synonymous (silent) variant that is not predicted by SpliceAI and varSEAK to impact splicing (BP7).The filtering allele frequency (the lower threshold of the 95% CI of 799/30614) of the c.303G>A variant in RAG1 is 0.02460 for South Asian chromosomes by gnomAD v2.1.1 which is higher than the ClinGen SCID VCEP threshold (>0.00872) for BA1 and therefore meets this criterion (BA1). Additionally, 76 homozygous individuals were reported (BS2_Supporting is met). In summary, this variant is classified as a Benign for autosomal recessive SCID based on ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP (specification version 1.0): BA1, BS2_Supporting, and BP7. LINK:https://erepo.genome.network/evrepo/ui/classification/CA293046/MONDO:0000572/123

• Frequency:
  • Genomes: 𝑓 0.016 (37 hom., cov: 32)
  • Exomes 𝑓: 0.022 (440 hom.)
• Consequence: RAG1 NM_000448.3 synonymous
• Clinical Significance: Benign reviewed by expert panel B:8
• Conservation: PhyloP100: -0.753

Genes affected

RAG1 (HGNC:9831): (recombination activating 1) The protein encoded by this gene is involved in activation of immunoglobulin V-D-J recombination. The encoded protein is involved in recognition of the DNA substrate, but stable binding and cleavage activity also requires RAG2. Defects in this gene can be the cause of several diseases. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP7: For more information check the summary or visit ClinGen Evidence Repository.
• BS2: For more information check the summary or visit ClinGen Evidence Repository.
• BA1: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAG1	NM_000448.3	c.303G>A	p.Ala101Ala	synonymous_variant	Exon 2 of 2	ENST00000299440.6	NP_000439.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAG1	ENST00000299440.6	c.303G>A	p.Ala101Ala	synonymous_variant	Exon 2 of 2	1	NM_000448.3	ENSP00000299440.5

Frequencies

GnomAD3 genomes AF: 0.0161 AC: 2456 AN: 152130 Hom.: 37 Cov.: 32

Gnomad AFR AF: 0.00406

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0132

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0266

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0144

GnomAD2 exomes AF: 0.0169 AC: 4249 AN: 251226 AF XY: 0.0179

Gnomad AFR exome AF: 0.00332

Gnomad AMR exome AF: 0.00850

Gnomad ASJ exome AF: 0.00933

Gnomad EAS exome AF: 0.000163

Gnomad FIN exome AF: 0.00998

Gnomad NFE exome AF: 0.0236

Gnomad OTH exome AF: 0.0173

GnomAD4 exome AF: 0.0222 AC: 32435 AN: 1461888 Hom.: 440 Cov.: 31 AF XY: 0.0225 AC XY: 16332 AN XY: 727248

Gnomad4 AFR exome AF: 0.00317 AC: 106 AN: 33480

Gnomad4 AMR exome AF: 0.00908 AC: 406 AN: 44724

Gnomad4 ASJ exome AF: 0.0103 AC: 270 AN: 26136

Gnomad4 EAS exome AF: 0.000277 AC: 11 AN: 39700

Gnomad4 SAS exome AF: 0.0266 AC: 2298 AN: 86258

Gnomad4 FIN exome AF: 0.0110 AC: 587 AN: 53420

Gnomad4 NFE exome AF: 0.0247 AC: 27437 AN: 1112006

Gnomad4 Remaining exome AF: 0.0201 AC: 1213 AN: 60396

GnomAD4 genome AF: 0.0161 AC: 2451 AN: 152248 Hom.: 37 Cov.: 32 AF XY: 0.0155 AC XY: 1153 AN XY: 74438

Gnomad4 AFR AF: 0.00404 AC: 0.00404449 AN: 0.00404449

Gnomad4 AMR AF: 0.0131 AC: 0.0131441 AN: 0.0131441

Gnomad4 ASJ AF: 0.0127 AC: 0.0126728 AN: 0.0126728

Gnomad4 EAS AF: 0.000386 AC: 0.000385654 AN: 0.000385654

Gnomad4 SAS AF: 0.0262 AC: 0.0262172 AN: 0.0262172

Gnomad4 FIN AF: 0.0103 AC: 0.0102714 AN: 0.0102714

Gnomad4 NFE AF: 0.0257 AC: 0.0256968 AN: 0.0256968

Gnomad4 OTH AF: 0.0142 AC: 0.0142045 AN: 0.0142045

Alfa AF: 0.0199 Hom.: 100

Bravo AF: 0.0150

Asia WGS AF: 0.0130 AC: 46 AN: 3478

EpiCase AF: 0.0282

EpiControl AF: 0.0277

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: reviewed by expert panel

Submissions by phenotype

not specified Benign:2

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 05, 2013

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided Benign:2

Nov 01, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Recombinase activating gene 1 deficiency Benign:1

Nov 14, 2023

ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen

Significance: Benign

Review Status: reviewed by expert panel

Collection Method: curation

The c.303G>A (p.Ala101=) variant (NM_000022.4) is a synonymous (silent) variant that is not predicted by SpliceAI and varSEAK to impact splicing (BP7). The filtering allele frequency (the lower threshold of the 95% CI of 799/30614) of the c.303G>A variant in RAG1 is 0.02460 for South Asian chromosomes by gnomAD v2.1.1 which is higher than the ClinGen SCID VCEP threshold (>0.00872) for BA1 and therefore meets this criterion (BA1). Additionally, 76 homozygous individuals were reported (BS2_Supporting is met). In summary, this variant is classified as a Benign for autosomal recessive SCID based on ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP (specification version 1.0): BA1, BS2_Supporting, and BP7. -

Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Histiocytic medullary reticulosis Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive;C2673536:Combined immunodeficiency with skin granulomas Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.67
DANN	Benign	0.84
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4151025; hg19: chr11-36595157; COSMIC: COSV104408578; COSMIC: COSV104408578;