3-161280709-A-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374187	XR_001740993.2	n.10929-4008A>G		intron_variant	Intron 2 of 2
LOC105374187	XR_001740994.2	n.993-4008A>G		intron_variant	Intron 1 of 2
LOC105374187	XR_007096150.1	n.993-4008A>G		intron_variant	Intron 1 of 1
LOC105374187	XR_007096151.1	n.10207-4008A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;