rs912062

chr9-841152-C-Achr9-841152-C-Gchr9-841152-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 0.888 in 151,944 control chromosomes in the GnomAD database, including 60,228 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 0.89 (60228 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.931 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: 0.888 AC: 134859 AN: 151826 Hom.: 60188 Cov.: 29

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.888 AC: 134957 AN: 151944 Hom.: 60228 Cov.: 29 AF XY: 0.887 AC XY: 65830 AN XY: 74256

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.937

Gnomad4 OTH AF: 0.895

Alfa AF: 0.926 Hom.: 87238

Bravo AF: 0.877

Asia WGS AF: 0.830 AC: 2887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.59
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs912062; hg19: chr9-841152;