rs7910642

Variant names:

• chr10-99781822-G-A
• rs7910642

Your query was ambiguous. Multiple possible variants found:

• chr10-99781822-G-A
• chr10-99781822-G-T

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 0.123 in 152,244 control chromosomes in the GnomAD database, including 1,307 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 0.12 (1307 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.245
• Publications: 7 publications found

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 = 0.279 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: 0.123 AC: 18755 AN: 152124 Hom.: 1300 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.123 AC: 18794 AN: 152244 Hom.: 1307 Cov.: 33 AF XY: 0.125 AC XY: 9299 AN XY: 74444

African (AFR) AF: 0.127 AC: 5290 AN: 41536

American (AMR) AF: 0.104 AC: 1596 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3472

East Asian (EAS) AF: 0.291 AC: 1510 AN: 5182

South Asian (SAS) AF: 0.143 AC: 693 AN: 4830

European-Finnish (FIN) AF: 0.126 AC: 1333 AN: 10592

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7631 AN: 68014

Other (OTH) AF: 0.117 AC: 246 AN: 2110

Alfa AF: 0.120 Hom.: 153

Bravo AF: 0.124

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs7910642; hg19: chr10-101541579;