rs17118064

Variant names:

• chr14-22457498-G-A
• rs17118064

Your query was ambiguous. Multiple possible variants found:

• chr14-22457498-G-A
• chr14-22457498-G-C
• chr14-22457498-G-T

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 0.087 in 150,942 control chromosomes in the GnomAD database, including 679 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 0.087 (679 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22457498G>A		intragenic_variant
TRD		n.22457498G>A		intragenic_variant
TRD-AS1	NR_148361.1	n.225+23743C>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+23743C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13127 AN: 150824 Hom.: 677 Cov.: 25

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0252

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0732

Gnomad OTH AF: 0.0921

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

GnomAD4 genome AF: 0.0870 AC: 13133 AN: 150942 Hom.: 679 Cov.: 25 AF XY: 0.0856 AC XY: 6309 AN XY: 73694

African (AFR) AF: 0.142 AC: 5833 AN: 40952

American (AMR) AF: 0.0768 AC: 1154 AN: 15034

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3466

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5172

South Asian (SAS) AF: 0.0246 AC: 117 AN: 4764

European-Finnish (FIN) AF: 0.0624 AC: 652 AN: 10448

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0732 AC: 4962 AN: 67806

Other (OTH) AF: 0.0916 AC: 192 AN: 2096

Alfa AF: 0.0761 Hom.: 503

Bravo AF: 0.0911

Asia WGS AF: 0.0220 AC: 78 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	0.97
DANN	Benign	0.52
PhyloP100		-0.36
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: rs17118064; hg19: chr14-22926490;