chr16-30826275-C-T

Variant names:

• chr16-30826275-C-T
• rs12926237

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 0.479 in 151,884 control chromosomes in the GnomAD database, including 21,679 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 0.48 (21679 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 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: 0.480 AC: 72785 AN: 151766 Hom.: 21664 Cov.: 30

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.479 AC: 72816 AN: 151884 Hom.: 21679 Cov.: 30 AF XY: 0.480 AC XY: 35635 AN XY: 74196

African (AFR) AF: 0.126 AC: 5204 AN: 41436

American (AMR) AF: 0.650 AC: 9905 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2033 AN: 3470

East Asian (EAS) AF: 0.910 AC: 4684 AN: 5150

South Asian (SAS) AF: 0.267 AC: 1283 AN: 4806

European-Finnish (FIN) AF: 0.627 AC: 6609 AN: 10542

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41249 AN: 67946

Other (OTH) AF: 0.536 AC: 1127 AN: 2102

Alfa AF: 0.579 Hom.: 9470

Bravo AF: 0.477

Asia WGS AF: 0.520 AC: 1812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.44
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs12926237; hg19: chr16-30837596;