rs10460960

Variant names:

• chr3-42267243-G-A
• rs10460960

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

ACMG classification

Verdict is Benign. Variant got -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.

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

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

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.937

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.843

Alfa AF: 0.857 Hom.: 24999

Bravo AF: 0.802

Asia WGS AF: 0.782 AC: 2721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10460960; hg19: chr3-42308735;