rs17794083

Variant names:

• chr14-22457927-C-A
• rs17794083

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 0.136 in 151,006 control chromosomes in the GnomAD database, including 1,525 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 0.14 (1525 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 3 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=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22457927C>A		intragenic_variant
TRD		n.22457927C>A		intragenic_variant
TRD-AS1	NR_148361.1	n.225+23314G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.225+23314G>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20555 AN: 150888 Hom.: 1522 Cov.: 26

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.00965

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.136 AC: 20575 AN: 151006 Hom.: 1525 Cov.: 26 AF XY: 0.132 AC XY: 9758 AN XY: 73822

African (AFR) AF: 0.109 AC: 4487 AN: 41000

American (AMR) AF: 0.110 AC: 1655 AN: 15080

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 462 AN: 3460

East Asian (EAS) AF: 0.00947 AC: 49 AN: 5172

South Asian (SAS) AF: 0.105 AC: 505 AN: 4790

European-Finnish (FIN) AF: 0.106 AC: 1102 AN: 10438

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11767 AN: 67764

Other (OTH) AF: 0.132 AC: 278 AN: 2100

Alfa AF: 0.156 Hom.: 1035

Bravo AF: 0.136

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	10
DANN	Benign	0.63
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17794083; hg19: chr14-22926919;