9-126179842-G-C

Variant names:

• chr9-126179842-G-C
• rs10987185

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 0.665 in 151,780 control chromosomes in the GnomAD database, including 33,660 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 (33660 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 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: 0.665 AC: 100880 AN: 151662 Hom.: 33631 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.665 AC: 100957 AN: 151780 Hom.: 33660 Cov.: 31 AF XY: 0.667 AC XY: 49460 AN XY: 74194

African (AFR) AF: 0.633 AC: 26215 AN: 41424

American (AMR) AF: 0.702 AC: 10724 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2101 AN: 3464

East Asian (EAS) AF: 0.711 AC: 3663 AN: 5152

South Asian (SAS) AF: 0.658 AC: 3163 AN: 4810

European-Finnish (FIN) AF: 0.690 AC: 7279 AN: 10548

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45427 AN: 67800

Other (OTH) AF: 0.680 AC: 1434 AN: 2110

Alfa AF: 0.661 Hom.: 3650

Bravo AF: 0.668

Asia WGS AF: 0.650 AC: 2257 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.47
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10987185; hg19: chr9-128942121;