chr16-10856669-A-T

Variant names:

• chr16-10856669-A-T
• rs9937955

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 0.67 in 151,862 control chromosomes in the GnomAD database, including 36,388 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 0.67 (36388 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101747 AN: 151744 Hom.: 36376 Cov.: 30

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.670 AC: 101796 AN: 151862 Hom.: 36388 Cov.: 30 AF XY: 0.664 AC XY: 49267 AN XY: 74220

African (AFR) AF: 0.511 AC: 21139 AN: 41360

American (AMR) AF: 0.547 AC: 8355 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2775 AN: 3472

East Asian (EAS) AF: 0.179 AC: 923 AN: 5168

South Asian (SAS) AF: 0.617 AC: 2964 AN: 4804

European-Finnish (FIN) AF: 0.801 AC: 8448 AN: 10548

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54722 AN: 67932

Other (OTH) AF: 0.698 AC: 1472 AN: 2110

Alfa AF: 0.728 Hom.: 5161

Bravo AF: 0.639

Asia WGS AF: 0.451 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.34
DANN	Benign	0.79
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs9937955; hg19: chr16-10950526;