16-50403617-C-T

Variant names:

• chr16-50403617-C-T
• rs9941219

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 0.107 in 152,242 control chromosomes in the GnomAD database, including 893 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 0.11 (893 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 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: 0.107 AC: 16221 AN: 152124 Hom.: 888 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0826

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.0329

Gnomad SAS AF: 0.0835

Gnomad FIN AF: 0.0765

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.107 AC: 16251 AN: 152242 Hom.: 893 Cov.: 33 AF XY: 0.105 AC XY: 7799 AN XY: 74436

African (AFR) AF: 0.129 AC: 5365 AN: 41532

American (AMR) AF: 0.0824 AC: 1261 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0988 AC: 343 AN: 3470

East Asian (EAS) AF: 0.0332 AC: 172 AN: 5180

South Asian (SAS) AF: 0.0844 AC: 407 AN: 4822

European-Finnish (FIN) AF: 0.0765 AC: 812 AN: 10608

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7573 AN: 68010

Other (OTH) AF: 0.103 AC: 217 AN: 2112

Alfa AF: 0.107 Hom.: 1020

Bravo AF: 0.106

Asia WGS AF: 0.0480 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.029
DANN	Benign	0.79
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs9941219; hg19: chr16-50437528;