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. Variant got -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

Genes affected

ENSG00000282890 (HGNC:58158):

ACMG classification

Verdict is Benign. Variant got -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.

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.303-1518G>A		intron_variant	Intron 1 of 4	5

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

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.573

Alfa AF: 0.554 Hom.: 29302

Bravo AF: 0.583

Asia WGS AF: 0.666 AC: 2308 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4952931; hg19: chr2-49171837;