14-21728267-C-A

Variant names:

• chr14-21728267-C-A
• rs10132760

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 0.582 in 152,050 control chromosomes in the GnomAD database, including 27,065 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 (27065 hom., cov: 32)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• 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=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 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: 0.582 AC: 88451 AN: 151932 Hom.: 27061 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.582 AC: 88485 AN: 152050 Hom.: 27065 Cov.: 32 AF XY: 0.575 AC XY: 42708 AN XY: 74332

African (AFR) AF: 0.393 AC: 16295 AN: 41444

American (AMR) AF: 0.590 AC: 9026 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2212 AN: 3466

East Asian (EAS) AF: 0.528 AC: 2725 AN: 5164

South Asian (SAS) AF: 0.600 AC: 2891 AN: 4820

European-Finnish (FIN) AF: 0.541 AC: 5716 AN: 10566

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47545 AN: 67980

Other (OTH) AF: 0.612 AC: 1288 AN: 2104

Alfa AF: 0.631 Hom.: 9027

Bravo AF: 0.577

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.51
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10132760; hg19: chr14-22196541;