16-26874766-C-T

Variant names:

• chr16-26874766-C-T
• rs723876

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 0.486 in 152,080 control chromosomes in the GnomAD database, including 21,434 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 0.49 (21434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 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: 0.486 AC: 73832 AN: 151962 Hom.: 21425 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.486 AC: 73859 AN: 152080 Hom.: 21434 Cov.: 32 AF XY: 0.485 AC XY: 36039 AN XY: 74330

African (AFR) AF: 0.151 AC: 6260 AN: 41512

American (AMR) AF: 0.621 AC: 9502 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1895 AN: 5162

South Asian (SAS) AF: 0.491 AC: 2362 AN: 4810

European-Finnish (FIN) AF: 0.606 AC: 6397 AN: 10548

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43647 AN: 67974

Other (OTH) AF: 0.514 AC: 1083 AN: 2108

Alfa AF: 0.358 Hom.: 1442

Bravo AF: 0.475

Asia WGS AF: 0.405 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs723876; hg19: chr16-26886087;