16-26500225-C-T

Variant names:

• chr16-26500225-C-T
• rs1012650

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 0.621 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
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.744 AC: 30439 AN: 40928

American (AMR) AF: 0.574 AC: 8679 AN: 15126

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1901 AN: 3462

East Asian (EAS) AF: 0.611 AC: 3104 AN: 5080

South Asian (SAS) AF: 0.459 AC: 2179 AN: 4746

European-Finnish (FIN) AF: 0.628 AC: 6429 AN: 10240

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.576 AC: 38980 AN: 67714

Other (OTH) AF: 0.576 AC: 1199 AN: 2082

Alfa AF: 0.580 Hom.: 6322

Bravo AF: 0.624

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.24
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs1012650; hg19: chr16-26511546;