rs9937955

Positions:

• chr16-10856669-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 0.67 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.698

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9937955; hg19: chr16-10950526;