rs3925065

Variant names:

• chr3-157949325-G-A
• rs3925065
• ENST00000651134.1:n.662+12648C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-157949325-G-A
• chr3-157949325-G-T

Variant summary

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

The ENST00000651134.1(ENSG00000242536):​n.662+12648C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,052 control chromosomes in the GnomAD database, including 11,973 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 0.38 (11973 hom., cov: 32)
• Consequence: ENSG00000242536 ENST00000651134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 4 publications found

Genes affected

ENSG00000242536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651134.1. 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
	ENSG00000242536	ENST00000651134.1		n.662+12648C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58224 AN: 151934 Hom.: 11970 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.383 AC: 58259 AN: 152052 Hom.: 11973 Cov.: 32 AF XY: 0.385 AC XY: 28589 AN XY: 74338

African (AFR) AF: 0.230 AC: 9548 AN: 41498

American (AMR) AF: 0.375 AC: 5726 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2341 AN: 5158

South Asian (SAS) AF: 0.521 AC: 2509 AN: 4818

European-Finnish (FIN) AF: 0.419 AC: 4428 AN: 10568

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30881 AN: 67948

Other (OTH) AF: 0.382 AC: 805 AN: 2108

Alfa AF: 0.444 Hom.: 8677

Bravo AF: 0.374

Asia WGS AF: 0.502 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.8
DANN	Benign	0.75
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs3925065; hg19: chr3-157667114; COSMIC: COSV51051917;