chr10-99781822-G-A

Variant names:

• chr10-99781822-G-A
• rs7910642

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 0.123 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.123 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

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.117

Alfa AF: 0.120 Hom.: 152

Bravo AF: 0.124

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7910642; hg19: chr10-101541579;