14-21960136-C-A

Variant names:

• chr14-21960136-C-A
• rs12433492

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 0.578 in 151,812 control chromosomes in the GnomAD database, including 25,926 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 0.58 (25926 hom., cov: 30)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 4 publications found

Genes affected

TRA (HGNC:12027):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 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: 0.578 AC: 87673 AN: 151694 Hom.: 25901 Cov.: 30

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.578 AC: 87741 AN: 151812 Hom.: 25926 Cov.: 30 AF XY: 0.573 AC XY: 42553 AN XY: 74200

African (AFR) AF: 0.689 AC: 28503 AN: 41362

American (AMR) AF: 0.481 AC: 7341 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2117 AN: 3462

East Asian (EAS) AF: 0.409 AC: 2116 AN: 5174

South Asian (SAS) AF: 0.600 AC: 2882 AN: 4804

European-Finnish (FIN) AF: 0.533 AC: 5608 AN: 10526

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37262 AN: 67924

Other (OTH) AF: 0.576 AC: 1213 AN: 2106

Alfa AF: 0.562 Hom.: 4720

Bravo AF: 0.578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.87
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs12433492; hg19: chr14-22428364;