rs10460960

Variant names:

• chr3-42267243-G-A
• rs10460960
• ENST00000807313.1:n.1232+852G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-42267243-G-A
• chr3-42267243-G-T

Variant summary

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

The ENST00000807313.1(ENSG00000281160):​n.1232+852G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,036 control chromosomes in the GnomAD database, including 51,983 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 0.82 (51983 hom., cov: 29)
• Consequence: ENSG00000281160 ENST00000807313.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 17 publications found

Genes affected

ENSG00000281160 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807313.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000281160	ENST00000807313.1		n.1232+852G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124671 AN: 151918 Hom.: 51962 Cov.: 29

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.820 AC: 124743 AN: 152036 Hom.: 51983 Cov.: 29 AF XY: 0.823 AC XY: 61138 AN XY: 74310

African (AFR) AF: 0.681 AC: 28187 AN: 41420

American (AMR) AF: 0.819 AC: 12510 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3252 AN: 3470

East Asian (EAS) AF: 0.706 AC: 3639 AN: 5154

South Asian (SAS) AF: 0.863 AC: 4145 AN: 4802

European-Finnish (FIN) AF: 0.913 AC: 9665 AN: 10590

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60463 AN: 68006

Other (OTH) AF: 0.843 AC: 1776 AN: 2106

Alfa AF: 0.858 Hom.: 28207

Bravo AF: 0.802

Asia WGS AF: 0.782 AC: 2721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.59
DANN	Benign	0.47
PhyloP100		-0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10460960;

hg19: chr3-42308735;