16-50808166-T-C

Variant names:

• chr16-50808166-T-C
• rs4785452

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 0.508 in 151,400 control chromosomes in the GnomAD database, including 20,000 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 0.51 (20000 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 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: 0.508 AC: 76885 AN: 151282 Hom.: 19979 Cov.: 30

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.508 AC: 76959 AN: 151400 Hom.: 20000 Cov.: 30 AF XY: 0.504 AC XY: 37262 AN XY: 73936

African (AFR) AF: 0.532 AC: 21834 AN: 41024

American (AMR) AF: 0.498 AC: 7592 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2272 AN: 3470

East Asian (EAS) AF: 0.185 AC: 950 AN: 5148

South Asian (SAS) AF: 0.474 AC: 2283 AN: 4814

European-Finnish (FIN) AF: 0.486 AC: 5093 AN: 10470

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.518 AC: 35161 AN: 67910

Other (OTH) AF: 0.508 AC: 1070 AN: 2106

Alfa AF: 0.517 Hom.: 83948

Bravo AF: 0.508

Asia WGS AF: 0.358 AC: 1246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.16
DANN	Benign	0.34
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4785452; hg19: chr16-50842077;