16-13882499-T-C

Variant names:

• chr16-13882499-T-C
• rs2113334

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 0.633 in 152,110 control chromosomes in the GnomAD database, including 32,953 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 0.63 (32953 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.766
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 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: 0.633 AC: 96199 AN: 151992 Hom.: 32957 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.633 AC: 96225 AN: 152110 Hom.: 32953 Cov.: 31 AF XY: 0.632 AC XY: 46995 AN XY: 74346

African (AFR) AF: 0.374 AC: 15516 AN: 41474

American (AMR) AF: 0.745 AC: 11378 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2673 AN: 3472

East Asian (EAS) AF: 0.349 AC: 1803 AN: 5170

South Asian (SAS) AF: 0.531 AC: 2559 AN: 4820

European-Finnish (FIN) AF: 0.765 AC: 8085 AN: 10566

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51989 AN: 68012

Other (OTH) AF: 0.654 AC: 1380 AN: 2110

Alfa AF: 0.718 Hom.: 171395

Bravo AF: 0.620

Asia WGS AF: 0.411 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	10
DANN	Benign	0.76
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs2113334; hg19: chr16-13976356;