rs4952931

Variant names:

• chr2-48944698-G-A
• rs4952931
• ENST00000634588.1:n.303-1518G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-48944698-G-A
• chr2-48944698-G-C

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.303-1518G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 150,052 control chromosomes in the GnomAD database, including 25,651 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 0.59 (25651 hom., cov: 27)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 1 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634588.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282890	ENST00000634588.1	TSL:5	n.303-1518G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.585 AC: 87720 AN: 149946 Hom.: 25617 Cov.: 27

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.585 AC: 87796 AN: 150052 Hom.: 25651 Cov.: 27 AF XY: 0.590 AC XY: 43161 AN XY: 73096

African (AFR) AF: 0.613 AC: 24966 AN: 40738

American (AMR) AF: 0.623 AC: 9373 AN: 15042

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1775 AN: 3456

East Asian (EAS) AF: 0.714 AC: 3641 AN: 5096

South Asian (SAS) AF: 0.640 AC: 3032 AN: 4736

European-Finnish (FIN) AF: 0.627 AC: 6316 AN: 10066

Middle Eastern (MID) AF: 0.531 AC: 153 AN: 288

European-Non Finnish (NFE) AF: 0.547 AC: 37001 AN: 67632

Other (OTH) AF: 0.573 AC: 1196 AN: 2088

Alfa AF: 0.556 Hom.: 39583

Bravo AF: 0.583

Asia WGS AF: 0.666 AC: 2308 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.76
DANN	Benign	0.67
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs4952931; hg19: chr2-49171837;