16-50816936-T-C

Variant names:

• chr16-50816936-T-C
• rs2032688

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 0.952 in 152,264 control chromosomes in the GnomAD database, including 69,264 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 0.95 (69264 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.964 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: 0.953 AC: 144926 AN: 152144 Hom.: 69219 Cov.: 31

Gnomad AFR AF: 0.955

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.947

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

GnomAD4 genome AF: 0.952 AC: 145031 AN: 152264 Hom.: 69264 Cov.: 31 AF XY: 0.948 AC XY: 70553 AN XY: 74448

African (AFR) AF: 0.954 AC: 39647 AN: 41544

American (AMR) AF: 0.971 AC: 14851 AN: 15298

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

East Asian (EAS) AF: 0.857 AC: 4440 AN: 5178

South Asian (SAS) AF: 0.713 AC: 3432 AN: 4816

European-Finnish (FIN) AF: 0.955 AC: 10132 AN: 10608

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

European-Non Finnish (NFE) AF: 0.970 AC: 65981 AN: 68030

Other (OTH) AF: 0.946 AC: 1998 AN: 2112

Alfa AF: 0.968 Hom.: 3308

Bravo AF: 0.958

Asia WGS AF: 0.788 AC: 2744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.66
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2032688; hg19: chr16-50850847;