rs2254896

Variant names:

• chr14-21807880-G-A
• rs2254896

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 0.488 in 151,884 control chromosomes in the GnomAD database, including 19,087 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 0.49 (19087 hom., cov: 31)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74159 AN: 151764 Hom.: 19095 Cov.: 31

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.488 AC: 74155 AN: 151884 Hom.: 19087 Cov.: 31 AF XY: 0.492 AC XY: 36527 AN XY: 74224

African (AFR) AF: 0.356 AC: 14742 AN: 41408

American (AMR) AF: 0.416 AC: 6356 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1813 AN: 3466

East Asian (EAS) AF: 0.374 AC: 1936 AN: 5174

South Asian (SAS) AF: 0.404 AC: 1942 AN: 4804

European-Finnish (FIN) AF: 0.666 AC: 7015 AN: 10540

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.571 AC: 38756 AN: 67906

Other (OTH) AF: 0.472 AC: 998 AN: 2114

Alfa AF: 0.510 Hom.: 6724

Bravo AF: 0.466

Asia WGS AF: 0.446 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.61
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2254896; hg19: chr14-22276052;