rs10015924

Variant names:

• chr4-122098465-T-C
• rs10015924

Variant summary

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

The variant allele was found at a frequency of 0.674 in 152,116 control chromosomes in the GnomAD database, including 34,774 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 0.67 (34774 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 5 publications found

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 (SAS) allele frequency at 95% confidence interval = 0.763 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: 0.674 AC: 102441 AN: 151998 Hom.: 34743 Cov.: 33

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.674 AC: 102526 AN: 152116 Hom.: 34774 Cov.: 33 AF XY: 0.676 AC XY: 50240 AN XY: 74368

African (AFR) AF: 0.710 AC: 29478 AN: 41510

American (AMR) AF: 0.736 AC: 11245 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2115 AN: 3470

East Asian (EAS) AF: 0.707 AC: 3656 AN: 5174

South Asian (SAS) AF: 0.784 AC: 3775 AN: 4814

European-Finnish (FIN) AF: 0.602 AC: 6360 AN: 10568

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43726 AN: 67980

Other (OTH) AF: 0.667 AC: 1408 AN: 2110

Alfa AF: 0.688 Hom.: 8957

Bravo AF: 0.684

Asia WGS AF: 0.734 AC: 2554 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	3.5
DANN	Benign	0.53
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10015924; hg19: chr4-123019620;