chr16-26719846-T-C

Variant names:

• chr16-26719846-T-C
• rs695090

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 0.745 in 152,158 control chromosomes in the GnomAD database, including 42,445 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 0.75 (42445 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113372 AN: 152040 Hom.: 42438 Cov.: 33

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.745 AC: 113419 AN: 152158 Hom.: 42445 Cov.: 33 AF XY: 0.748 AC XY: 55655 AN XY: 74382

African (AFR) AF: 0.754 AC: 31292 AN: 41488

American (AMR) AF: 0.640 AC: 9791 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2451 AN: 3472

East Asian (EAS) AF: 0.757 AC: 3916 AN: 5176

South Asian (SAS) AF: 0.828 AC: 3984 AN: 4814

European-Finnish (FIN) AF: 0.837 AC: 8873 AN: 10598

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.746 AC: 50707 AN: 68008

Other (OTH) AF: 0.719 AC: 1516 AN: 2108

Alfa AF: 0.747 Hom.: 5491

Bravo AF: 0.726

Asia WGS AF: 0.792 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.76
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs695090; hg19: chr16-26731167;