rs10142594

Variant names:

• chr14-22307449-G-A
• rs10142594

Your query was ambiguous. Multiple possible variants found:

• chr14-22307449-G-A
• chr14-22307449-G-T

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 0.0531 in 151,218 control chromosomes in the GnomAD database, including 299 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 0.053 (299 hom., cov: 27)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22307449G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+93595C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0532 AC: 8033 AN: 151100 Hom.: 299 Cov.: 27

Gnomad AFR AF: 0.0183

Gnomad AMI AF: 0.0540

Gnomad AMR AF: 0.0485

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0736

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0531 AC: 8033 AN: 151218 Hom.: 299 Cov.: 27 AF XY: 0.0517 AC XY: 3821 AN XY: 73856

African (AFR) AF: 0.0182 AC: 749 AN: 41138

American (AMR) AF: 0.0485 AC: 732 AN: 15082

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 320 AN: 3450

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0284 AC: 136 AN: 4790

European-Finnish (FIN) AF: 0.0847 AC: 883 AN: 10430

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

European-Non Finnish (NFE) AF: 0.0736 AC: 4994 AN: 67854

Other (OTH) AF: 0.0682 AC: 143 AN: 2098

Alfa AF: 0.0561 Hom.: 166

Bravo AF: 0.0501

Asia WGS AF: 0.0160 AC: 55 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	9.5
DANN	Benign	0.76
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs10142594; hg19: chr14-22775868;