rs1922476

Variant names:

• chr2-48957188-G-A
• rs1922476
• ENST00000634588.1:n.492+10783G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-48957188-G-A
• chr2-48957188-G-C
• chr2-48957188-G-T

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.492+10783G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,004 control chromosomes in the GnomAD database, including 24,065 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 0.55 (24065 hom., cov: 31)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• Publications: 4 publications found

Genes affected

ENSG00000282890 (HGNC:58158):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282890	ENST00000634588.1	n.492+10783G>A		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83891 AN: 151888 Hom.: 24060 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.552 AC: 83929 AN: 152004 Hom.: 24065 Cov.: 31 AF XY: 0.556 AC XY: 41299 AN XY: 74278

African (AFR) AF: 0.386 AC: 15972 AN: 41428

American (AMR) AF: 0.654 AC: 10006 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1919 AN: 3472

East Asian (EAS) AF: 0.721 AC: 3717 AN: 5154

South Asian (SAS) AF: 0.587 AC: 2821 AN: 4808

European-Finnish (FIN) AF: 0.648 AC: 6852 AN: 10576

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40794 AN: 67962

Other (OTH) AF: 0.569 AC: 1199 AN: 2108

Alfa AF: 0.585 Hom.: 81987

Bravo AF: 0.548

Asia WGS AF: 0.632 AC: 2195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.65
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs1922476; hg19: chr2-49184327;