rs741711

Variant names:

• chr14-22385282-C-T
• rs741711

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 0.126 in 150,864 control chromosomes in the GnomAD database, including 1,364 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 0.13 (1364 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514473.2. 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
	TRD-AS1	NR_148361.1		n.226-2877G>A		intron	N/A
	TRD-AS1	NR_148362.1		n.290-2877G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000514473.2	TSL:2	n.226-2877G>A		intron	N/A
	TRD-AS1	ENST00000541008.6	TSL:4	n.277-2877G>A		intron	N/A
	TRD-AS1	ENST00000545670.5	TSL:4	n.276-2877G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19056 AN: 150744 Hom.: 1360 Cov.: 26

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.126 AC: 19074 AN: 150864 Hom.: 1364 Cov.: 26 AF XY: 0.126 AC XY: 9295 AN XY: 73634

African (AFR) AF: 0.155 AC: 6337 AN: 40928

American (AMR) AF: 0.179 AC: 2691 AN: 15026

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3462

East Asian (EAS) AF: 0.145 AC: 745 AN: 5152

South Asian (SAS) AF: 0.0991 AC: 472 AN: 4764

European-Finnish (FIN) AF: 0.103 AC: 1077 AN: 10430

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6940 AN: 67804

Other (OTH) AF: 0.136 AC: 285 AN: 2102

Alfa AF: 0.110 Hom.: 583

Bravo AF: 0.140

Asia WGS AF: 0.128 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.32
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs741711; hg19: chr14-22853685;