rs16947526

Variant names:

• chr16-74826658-C-T
• rs16947526

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 0.0759 in 152,142 control chromosomes in the GnomAD database, including 441 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 0.076 (441 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0838 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: 0.0760 AC: 11555 AN: 152024 Hom.: 442 Cov.: 32

Gnomad AFR AF: 0.0817

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0629

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.0658

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0856

Gnomad OTH AF: 0.0848

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

GnomAD4 genome AF: 0.0759 AC: 11551 AN: 152142 Hom.: 441 Cov.: 32 AF XY: 0.0745 AC XY: 5544 AN XY: 74396

Gnomad4 AFR AF: 0.0815

Gnomad4 AMR AF: 0.0628

Gnomad4 ASJ AF: 0.0539

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.0658

Gnomad4 NFE AF: 0.0856

Gnomad4 OTH AF: 0.0834

Alfa AF: 0.0846 Hom.: 635

Bravo AF: 0.0749

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16947526; hg19: chr16-74860556;