rs695090

Variant names:

• chr16-26719846-T-C
• rs695090

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 0.745 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.746 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

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.719

Alfa AF: 0.747 Hom.: 5260

Bravo AF: 0.726

Asia WGS AF: 0.792 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs695090; hg19: chr16-26731167;