chr1-183927827-T-C

Position:

• chr1-183927827-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001297671.3(RGL1):​c.*1535T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,376 control chromosomes in the GnomAD database, including 25,993 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.58 (25921 hom., cov: 32)
  • Exomes 𝑓: 0.58 (72 hom.)
• Consequence: RGL1 NM_001297671.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

RGL1 (HGNC:30281): (ral guanine nucleotide dissociation stimulator like 1) Predicted to be involved in regulation of catalytic activity. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGL1	NM_001297671.3	c.*1535T>C		3_prime_UTR_variant	18/18	ENST00000360851.4	NP_001284600.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGL1	ENST00000360851.4	c.*1535T>C		3_prime_UTR_variant	18/18	1	NM_001297671.3	ENSP00000354097	P1
RGL1	ENST00000304685.8	c.*1535T>C		3_prime_UTR_variant	19/19	1		ENSP00000303192

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88545 AN: 151826 Hom.: 25892 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.571

GnomAD4 exome AF: 0.581 AC: 251 AN: 432 Hom.: 72 Cov.: 0 AF XY: 0.604 AC XY: 157 AN XY: 260

Gnomad4 FIN exome AF: 0.577

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.583 AC: 88624 AN: 151944 Hom.: 25921 Cov.: 32 AF XY: 0.583 AC XY: 43267 AN XY: 74250

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.574

Alfa AF: 0.562 Hom.: 23591

Bravo AF: 0.576

Asia WGS AF: 0.575 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.22
DANN	Benign	0.45

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: rs4650; hg19: chr1-183896961;