14-21853868-G-T

Variant names:

• chr14-21853868-G-T
• rs760002

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 0.433 in 151,842 control chromosomes in the GnomAD database, including 14,776 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 0.43 (14776 hom., cov: 31)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.526 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: 0.433 AC: 65703 AN: 151724 Hom.: 14775 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.433 AC: 65734 AN: 151842 Hom.: 14776 Cov.: 31 AF XY: 0.428 AC XY: 31726 AN XY: 74162

African (AFR) AF: 0.512 AC: 21168 AN: 41370

American (AMR) AF: 0.536 AC: 8190 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3472

East Asian (EAS) AF: 0.370 AC: 1909 AN: 5166

South Asian (SAS) AF: 0.461 AC: 2214 AN: 4806

European-Finnish (FIN) AF: 0.268 AC: 2822 AN: 10524

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.393 AC: 26724 AN: 67920

Other (OTH) AF: 0.428 AC: 901 AN: 2106

Alfa AF: 0.412 Hom.: 1717

Bravo AF: 0.457

Asia WGS AF: 0.346 AC: 1201 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.57
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs760002; hg19: chr14-22322045;