rs4962728

Variant names:

• chr10-124320411-A-C
• rs4962728

Your query was ambiguous. Multiple possible variants found:

• chr10-124320411-A-C
• chr10-124320411-A-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 0.498 in 152,056 control chromosomes in the GnomAD database, including 19,146 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 (19146 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 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: 0.498 AC: 75656 AN: 151938 Hom.: 19148 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.498 AC: 75683 AN: 152056 Hom.: 19146 Cov.: 32 AF XY: 0.496 AC XY: 36828 AN XY: 74308

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.522

Alfa AF: 0.431 Hom.: 2481

Bravo AF: 0.494

Asia WGS AF: 0.487 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.068
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4962728; hg19: chr10-126008980;