rs10490346

Variant names:

• chr2-45511404-T-C
• rs10490346
• NM_018079.5:c.1875-23073A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018079.5(SRBD1):​c.1875-23073A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 152,230 control chromosomes in the GnomAD database, including 559 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 0.068 (559 hom., cov: 32)
• Consequence: SRBD1 NM_018079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 0 publications found

Genes affected

SRBD1 (HGNC:25521): (S1 RNA binding domain 1) Predicted to enable mRNA binding activity. Predicted to be a structural constituent of ribosome. Predicted to be involved in translation. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018079.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRBD1	NM_018079.5	MANE Select	c.1875-23073A>G		intron	N/A	NP_060549.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRBD1	ENST00000263736.5	TSL:2 MANE Select	c.1875-23073A>G		intron	N/A	ENSP00000263736.4
	SRBD1	ENST00000475073.5	TSL:4	n.282-23073A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0682 AC: 10371 AN: 152112 Hom.: 558 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0314

Gnomad FIN AF: 0.0639

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.0723

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0681 AC: 10372 AN: 152230 Hom.: 559 Cov.: 32 AF XY: 0.0689 AC XY: 5125 AN XY: 74430

African (AFR) AF: 0.150 AC: 6242 AN: 41508

American (AMR) AF: 0.0494 AC: 755 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5190

South Asian (SAS) AF: 0.0308 AC: 149 AN: 4830

European-Finnish (FIN) AF: 0.0639 AC: 678 AN: 10608

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0324 AC: 2204 AN: 68022

Other (OTH) AF: 0.0716 AC: 151 AN: 2110

Alfa AF: 0.0630 Hom.: 83

Bravo AF: 0.0702

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.76
PhyloP100		-2.0
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

Other links and lift over

dbSNP: rs10490346; hg19: chr2-45738543;