rs10131293

Variant names:

• chr14-22461166-G-A
• rs10131293

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 0.147 in 149,806 control chromosomes in the GnomAD database, including 2,753 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 0.15 (2753 hom., cov: 23)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 2 publications found

Genes affected

TRA (HGNC:12027):

TRD (HGNC:12252):

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 = 0.341 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.225+20075C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000514473.2	TSL:2	n.225+20075C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22043 AN: 149688 Hom.: 2747 Cov.: 23

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.0521

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0989

Gnomad EAS AF: 0.000583

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0629

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0750

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.147 AC: 22071 AN: 149806 Hom.: 2753 Cov.: 23 AF XY: 0.144 AC XY: 10536 AN XY: 73222

African (AFR) AF: 0.345 AC: 13952 AN: 40392

American (AMR) AF: 0.105 AC: 1574 AN: 14944

Ashkenazi Jewish (ASJ) AF: 0.0989 AC: 341 AN: 3448

East Asian (EAS) AF: 0.000584 AC: 3 AN: 5138

South Asian (SAS) AF: 0.0263 AC: 124 AN: 4722

European-Finnish (FIN) AF: 0.0629 AC: 649 AN: 10312

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0750 AC: 5068 AN: 67570

Other (OTH) AF: 0.138 AC: 287 AN: 2084

Alfa AF: 0.0613 Hom.: 160

Bravo AF: 0.161

Asia WGS AF: 0.0360 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10131293; hg19: chr14-22930158;