16-81227181-C-T

Variant names:

• chr16-81227181-C-T
• rs9708919

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 0.42 in 151,824 control chromosomes in the GnomAD database, including 14,082 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 0.42 (14082 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63819 AN: 151708 Hom.: 14084 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.420 AC: 63831 AN: 151824 Hom.: 14082 Cov.: 31 AF XY: 0.413 AC XY: 30644 AN XY: 74200

African (AFR) AF: 0.345 AC: 14274 AN: 41364

American (AMR) AF: 0.393 AC: 5989 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1965 AN: 3470

East Asian (EAS) AF: 0.122 AC: 631 AN: 5180

South Asian (SAS) AF: 0.318 AC: 1533 AN: 4818

European-Finnish (FIN) AF: 0.400 AC: 4211 AN: 10516

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33633 AN: 67922

Other (OTH) AF: 0.461 AC: 970 AN: 2102

Alfa AF: 0.326 Hom.: 867

Bravo AF: 0.416

Asia WGS AF: 0.206 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.47
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs9708919; hg19: chr16-81260786;