rs741713

Variant names:

• chr14-22303362-C-A
• rs741713

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 0.643 in 150,462 control chromosomes in the GnomAD database, including 34,294 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 0.64 (34294 hom., cov: 24)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 4 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 (Cadd=0.411).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656379.1. You can select a different transcript below to see updated ACMG assignments.

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
	TRD-AS1	ENST00000656379.1		n.270+97682G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.643 AC: 96746 AN: 150344 Hom.: 34291 Cov.: 24

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.643 AC: 96763 AN: 150462 Hom.: 34294 Cov.: 24 AF XY: 0.652 AC XY: 47884 AN XY: 73448

African (AFR) AF: 0.318 AC: 12955 AN: 40776

American (AMR) AF: 0.760 AC: 11389 AN: 14986

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2349 AN: 3460

East Asian (EAS) AF: 0.869 AC: 4484 AN: 5162

South Asian (SAS) AF: 0.778 AC: 3691 AN: 4742

European-Finnish (FIN) AF: 0.810 AC: 8387 AN: 10354

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51364 AN: 67682

Other (OTH) AF: 0.670 AC: 1404 AN: 2096

Alfa AF: 0.720 Hom.: 58830

Bravo AF: 0.623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.41
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs741713;