chr14-21960136-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.21960136C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;