16-50239636-C-T

Variant names:

• chr16-50239636-C-T
• rs4444336

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 0.469 in 151,894 control chromosomes in the GnomAD database, including 17,898 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 0.47 (17898 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 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: 0.469 AC: 71160 AN: 151774 Hom.: 17880 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.469 AC: 71195 AN: 151894 Hom.: 17898 Cov.: 31 AF XY: 0.479 AC XY: 35545 AN XY: 74230

African (AFR) AF: 0.285 AC: 11813 AN: 41388

American (AMR) AF: 0.508 AC: 7748 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3468

East Asian (EAS) AF: 0.666 AC: 3430 AN: 5154

South Asian (SAS) AF: 0.633 AC: 3037 AN: 4794

European-Finnish (FIN) AF: 0.658 AC: 6943 AN: 10558

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35210 AN: 67956

Other (OTH) AF: 0.465 AC: 983 AN: 2112

Alfa AF: 0.492 Hom.: 30951

Bravo AF: 0.450

Asia WGS AF: 0.594 AC: 2063 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	1.4
DANN	Benign	0.48
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4444336; hg19: chr16-50273547;