rs10047878

Variant names:

• chr14-22319258-T-A
• rs10047878

Your query was ambiguous. Multiple possible variants found:

• chr14-22319258-T-A
• chr14-22319258-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.64 in 150,706 control chromosomes in the GnomAD database, including 31,922 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 (31922 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606

Genes affected

TRA (HGNC:12027):

TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22319258T>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+81786A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.640 AC: 96312 AN: 150588 Hom.: 31872 Cov.: 26

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.539

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.640 AC: 96416 AN: 150706 Hom.: 31922 Cov.: 26 AF XY: 0.642 AC XY: 47256 AN XY: 73578

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.642

Alfa AF: 0.599 Hom.: 3508

Bravo AF: 0.650

Asia WGS AF: 0.723 AC: 2512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10047878; hg19: chr14-22787690;