16-26500225-C-T

Variant names:

• chr16-26500225-C-T
• rs1012650

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.621 in 150,576 control chromosomes in the GnomAD database, including 29,503 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 0.62 (29503 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 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: 0.621 AC: 93433 AN: 150460 Hom.: 29482 Cov.: 27

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.621 AC: 93500 AN: 150576 Hom.: 29503 Cov.: 27 AF XY: 0.618 AC XY: 45345 AN XY: 73374

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.576

Alfa AF: 0.470 Hom.: 1457

Bravo AF: 0.624

Asia WGS AF: 0.511 AC: 1778 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	1.3
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1012650; hg19: chr16-26511546;