14-22323783-T-C

Position:

• chr14-22323783-T-C

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 0.528 in 150,674 control chromosomes in the GnomAD database, including 21,146 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 0.53 (21146 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

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 (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRA		n.22323783T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+77261A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.528 AC: 79447 AN: 150556 Hom.: 21129 Cov.: 26

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.528 AC: 79507 AN: 150674 Hom.: 21146 Cov.: 26 AF XY: 0.531 AC XY: 39064 AN XY: 73576

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.520

Alfa AF: 0.498 Hom.: 10243

Bravo AF: 0.531

Asia WGS AF: 0.651 AC: 2262 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	6.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11847479; hg19: chr14-22792215;