9-101460951-C-G

Variant names:

• chr9-101460951-C-G
• rs10819937

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 0.79 in 151,974 control chromosomes in the GnomAD database, including 47,800 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 0.79 (47800 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.790 AC: 119913 AN: 151856 Hom.: 47770 Cov.: 31

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.790 AC: 119997 AN: 151974 Hom.: 47800 Cov.: 31 AF XY: 0.785 AC XY: 58319 AN XY: 74298

African (AFR) AF: 0.820 AC: 33890 AN: 41354

American (AMR) AF: 0.661 AC: 10102 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3005 AN: 3470

East Asian (EAS) AF: 0.596 AC: 3081 AN: 5168

South Asian (SAS) AF: 0.796 AC: 3829 AN: 4810

European-Finnish (FIN) AF: 0.782 AC: 8265 AN: 10566

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55129 AN: 68018

Other (OTH) AF: 0.793 AC: 1673 AN: 2110

Alfa AF: 0.810 Hom.: 5936

Bravo AF: 0.777

Asia WGS AF: 0.677 AC: 2358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.036
DANN	Benign	0.59
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs10819937; hg19: chr9-104223233;