rs16947526

chr16-74826658-C-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 0.0759 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;