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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22492115A>G		intragenic_variant

Ensembl

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

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 v4.3

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;