16-50818521-T-C

Variant names:

• chr16-50818521-T-C
• rs2032687

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 0.961 in 152,168 control chromosomes in the GnomAD database, including 70,486 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 0.96 (70486 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.976 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: 0.961 AC: 146127 AN: 152048 Hom.: 70428 Cov.: 30

Gnomad AFR AF: 0.984

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.961 AC: 146248 AN: 152168 Hom.: 70486 Cov.: 30 AF XY: 0.956 AC XY: 71127 AN XY: 74390

African (AFR) AF: 0.984 AC: 40849 AN: 41520

American (AMR) AF: 0.974 AC: 14885 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3364 AN: 3472

East Asian (EAS) AF: 0.857 AC: 4422 AN: 5158

South Asian (SAS) AF: 0.713 AC: 3428 AN: 4806

European-Finnish (FIN) AF: 0.955 AC: 10109 AN: 10584

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.970 AC: 65988 AN: 68020

Other (OTH) AF: 0.953 AC: 2017 AN: 2116

Alfa AF: 0.971 Hom.: 6005

Bravo AF: 0.968

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.068
DANN	Benign	0.46
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2032687; hg19: chr16-50852432;