10-81189166-G-A

Variant names:

• chr10-81189166-G-A
• rs7899151

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 0.747 in 151,366 control chromosomes in the GnomAD database, including 42,393 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 0.75 (42393 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 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: 0.747 AC: 112993 AN: 151248 Hom.: 42371 Cov.: 30

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.747 AC: 113064 AN: 151366 Hom.: 42393 Cov.: 30 AF XY: 0.745 AC XY: 55103 AN XY: 73956

African (AFR) AF: 0.742 AC: 30703 AN: 41378

American (AMR) AF: 0.734 AC: 11168 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.878 AC: 3042 AN: 3466

East Asian (EAS) AF: 0.869 AC: 4486 AN: 5160

South Asian (SAS) AF: 0.693 AC: 3328 AN: 4800

European-Finnish (FIN) AF: 0.711 AC: 7484 AN: 10524

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50161 AN: 67518

Other (OTH) AF: 0.791 AC: 1665 AN: 2106

Alfa AF: 0.737 Hom.: 5076

Bravo AF: 0.753

Asia WGS AF: 0.783 AC: 2721 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.54
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7899151; hg19: chr10-82948922;