14-32911892-T-C

Variant names:

• chr14-32911892-T-C
• rs12146962

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 0.452 in 152,052 control chromosomes in the GnomAD database, including 16,053 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 0.45 (16053 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68626 AN: 151934 Hom.: 16044 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.452 AC: 68677 AN: 152052 Hom.: 16053 Cov.: 33 AF XY: 0.452 AC XY: 33598 AN XY: 74332

African (AFR) AF: 0.355 AC: 14711 AN: 41492

American (AMR) AF: 0.394 AC: 6020 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2450 AN: 3466

East Asian (EAS) AF: 0.421 AC: 2182 AN: 5178

South Asian (SAS) AF: 0.395 AC: 1901 AN: 4814

European-Finnish (FIN) AF: 0.504 AC: 5319 AN: 10560

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34345 AN: 67964

Other (OTH) AF: 0.488 AC: 1029 AN: 2108

Alfa AF: 0.490 Hom.: 63283

Bravo AF: 0.439

Asia WGS AF: 0.445 AC: 1549 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12146962; hg19: chr14-33381098;