rs1686947

chr10-39554330-A-Gchr10-39554330-A-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 0.931 in 149,292 control chromosomes in the GnomAD database, including 64,684 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 0.93 (64684 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=3.245).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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: 0.931 AC: 138807 AN: 149174 Hom.: 64628 Cov.: 31

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.939

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.948

Gnomad MID AF: 0.901

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.931 AC: 138920 AN: 149292 Hom.: 64684 Cov.: 31 AF XY: 0.932 AC XY: 67920 AN XY: 72878

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.939

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.941

Gnomad4 FIN AF: 0.948

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.922

Alfa AF: 0.928 Hom.: 5559

Bravo AF: 0.928

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Cadd	Benign	3.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1686947; hg19: -;