16-50385293-C-A

Variant names:

• chr16-50385293-C-A
• rs8054797

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 0.283 in 151,960 control chromosomes in the GnomAD database, including 8,463 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 0.28 (8463 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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: 0.283 AC: 42986 AN: 151842 Hom.: 8469 Cov.: 31

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.283 AC: 43004 AN: 151960 Hom.: 8463 Cov.: 31 AF XY: 0.288 AC XY: 21398 AN XY: 74294

African (AFR) AF: 0.509 AC: 21051 AN: 41398

American (AMR) AF: 0.234 AC: 3571 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 310 AN: 3470

East Asian (EAS) AF: 0.729 AC: 3751 AN: 5148

South Asian (SAS) AF: 0.278 AC: 1341 AN: 4818

European-Finnish (FIN) AF: 0.237 AC: 2507 AN: 10568

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.143 AC: 9743 AN: 67966

Other (OTH) AF: 0.237 AC: 500 AN: 2110

Alfa AF: 0.231 Hom.: 4882

Bravo AF: 0.295

Asia WGS AF: 0.477 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.52
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs8054797; hg19: chr16-50419204;