rs10819937

Positions:

• chr9-101460951-C-G
• chr9-101460951-C-T

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 0.79 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.793

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10819937; hg19: chr9-104223233;