rs2082876

Positions:

• chr2-45542031-C-A
• chr2-45542031-C-T

Variant summary

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

The NM_018079.5(SRBD1):​c.1874+4701G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,038 control chromosomes in the GnomAD database, including 20,734 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 0.52 (20734 hom., cov: 32)
• Consequence: SRBD1 NM_018079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRBD1	NM_018079.5	c.1874+4701G>T		intron_variant		ENST00000263736.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRBD1	ENST00000263736.5	c.1874+4701G>T		intron_variant		2	NM_018079.5	P1
SRBD1	ENST00000475073.5	n.281+4701G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78439 AN: 151920 Hom.: 20722 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.516 AC: 78494 AN: 152038 Hom.: 20734 Cov.: 32 AF XY: 0.511 AC XY: 38012 AN XY: 74344

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.532

Alfa AF: 0.451 Hom.: 1935

Bravo AF: 0.513

Asia WGS AF: 0.311 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.49

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: rs2082876; hg19: chr2-45769170;