rs11845134

Variant names:

• chr14-22313945-C-T
• rs11845134

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 0.334 in 150,760 control chromosomes in the GnomAD database, including 12,509 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 0.33 (12509 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 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+87099G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50248 AN: 150642 Hom.: 12467 Cov.: 26

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.334 AC: 50344 AN: 150760 Hom.: 12509 Cov.: 26 AF XY: 0.334 AC XY: 24560 AN XY: 73620

African (AFR) AF: 0.707 AC: 28926 AN: 40886

American (AMR) AF: 0.229 AC: 3449 AN: 15054

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1045 AN: 3460

East Asian (EAS) AF: 0.136 AC: 705 AN: 5174

South Asian (SAS) AF: 0.283 AC: 1350 AN: 4768

European-Finnish (FIN) AF: 0.224 AC: 2327 AN: 10366

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11661 AN: 67760

Other (OTH) AF: 0.314 AC: 657 AN: 2092

Alfa AF: 0.222 Hom.: 13702

Bravo AF: 0.350

Asia WGS AF: 0.267 AC: 926 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs11845134; hg19: chr14-22782377;