rs2128997

Variant names:

• chr14-22492115-A-G
• rs2128997

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 0.273 in 151,164 control chromosomes in the GnomAD database, including 5,966 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 0.27 (5966 hom., cov: 27)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 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: 0.273 AC: 41309 AN: 151046 Hom.: 5968 Cov.: 27

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.273 AC: 41316 AN: 151164 Hom.: 5966 Cov.: 27 AF XY: 0.278 AC XY: 20502 AN XY: 73806

African (AFR) AF: 0.200 AC: 8233 AN: 41072

American (AMR) AF: 0.254 AC: 3846 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1304 AN: 3462

East Asian (EAS) AF: 0.518 AC: 2664 AN: 5138

South Asian (SAS) AF: 0.410 AC: 1964 AN: 4788

European-Finnish (FIN) AF: 0.308 AC: 3215 AN: 10434

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19082 AN: 67834

Other (OTH) AF: 0.315 AC: 658 AN: 2092

Alfa AF: 0.284 Hom.: 27125

Bravo AF: 0.265

Asia WGS AF: 0.440 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.1
DANN	Benign	0.51
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2128997; hg19: chr14-22961102;