rs12588739

Variant names:

• chr14-22297219-T-C
• rs12588739

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 0.0373 in 151,712 control chromosomes in the GnomAD database, including 138 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 0.037 (138 hom., cov: 27)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 1 publications found

Genes affected

TRA (HGNC:12027):

TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22297219T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.271-95837A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0372 AC: 5640 AN: 151594 Hom.: 137 Cov.: 27

Gnomad AFR AF: 0.0536

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.0511

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0343

Gnomad FIN AF: 0.0195

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0243

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0373 AC: 5659 AN: 151712 Hom.: 138 Cov.: 27 AF XY: 0.0378 AC XY: 2804 AN XY: 74152

African (AFR) AF: 0.0539 AC: 2225 AN: 41300

American (AMR) AF: 0.0273 AC: 414 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.0511 AC: 177 AN: 3462

East Asian (EAS) AF: 0.131 AC: 676 AN: 5172

South Asian (SAS) AF: 0.0342 AC: 164 AN: 4800

European-Finnish (FIN) AF: 0.0195 AC: 206 AN: 10546

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0243 AC: 1654 AN: 67938

Other (OTH) AF: 0.0445 AC: 94 AN: 2110

Alfa AF: 0.0300 Hom.: 273

Bravo AF: 0.0398

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.3
DANN	Benign	0.84
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs12588739; hg19: chr14-22765112;