XR_001740993.2:n.10929-4008A>G

Variant names:

• chr3-161280709-A-G
• rs7652267
• XR_001740993.2:n.10929-4008A>G

Variant summary

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

The XR_001740993.2(LOC105374187):​n.10929-4008A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,938 control chromosomes in the GnomAD database, including 19,099 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 0.50 (19099 hom., cov: 32)
• Consequence: LOC105374187 XR_001740993.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 8 publications found

Genes affected

LOC105374187 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75244 AN: 151820 Hom.: 19081 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.496 AC: 75293 AN: 151938 Hom.: 19099 Cov.: 32 AF XY: 0.496 AC XY: 36857 AN XY: 74238

African (AFR) AF: 0.541 AC: 22399 AN: 41408

American (AMR) AF: 0.538 AC: 8203 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1744 AN: 3472

East Asian (EAS) AF: 0.775 AC: 4003 AN: 5168

South Asian (SAS) AF: 0.529 AC: 2548 AN: 4814

European-Finnish (FIN) AF: 0.408 AC: 4300 AN: 10546

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30586 AN: 67968

Other (OTH) AF: 0.477 AC: 1008 AN: 2112

Alfa AF: 0.406 Hom.: 1814

Bravo AF: 0.506

Asia WGS AF: 0.586 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.61
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7652267; hg19: chr3-160998497; COSMIC: COSV70574727;