rs1686947

Variant names:

• chr10-39554330-A-G
• rs1686947

Your query was ambiguous. Multiple possible variants found:

• chr10-39554330-A-G
• chr10-39554330-A-T

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 0.931 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.913 AC: 37435 AN: 41010

American (AMR) AF: 0.939 AC: 13937 AN: 14840

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3165 AN: 3416

East Asian (EAS) AF: 0.955 AC: 4813 AN: 5038

South Asian (SAS) AF: 0.941 AC: 4522 AN: 4808

European-Finnish (FIN) AF: 0.948 AC: 10013 AN: 10564

Middle Eastern (MID) AF: 0.904 AC: 264 AN: 292

European-Non Finnish (NFE) AF: 0.936 AC: 62082 AN: 66344

Other (OTH) AF: 0.922 AC: 1911 AN: 2072

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

Other links and lift over

dbSNP: rs1686947; hg19: -;