rs10162417

Variant names:

• chr14-22460708-T-G
• rs10162417

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 151,030 control chromosomes in the GnomAD database, including 2,781 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 (2781 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• 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 (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22460708T>G		intragenic_variant
TRD		n.22460708T>G		intragenic_variant
TRD-AS1	NR_148361.1	n.225+20533A>C		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+20533A>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22244 AN: 150912 Hom.: 2775 Cov.: 26

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.0518

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0984

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.0624

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: 22272 AN: 151030 Hom.: 2781 Cov.: 26 AF XY: 0.144 AC XY: 10635 AN XY: 73816

African (AFR) AF: 0.346 AC: 14117 AN: 40838

American (AMR) AF: 0.104 AC: 1578 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.0984 AC: 340 AN: 3456

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0265 AC: 127 AN: 4792

European-Finnish (FIN) AF: 0.0624 AC: 655 AN: 10496

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

European-Non Finnish (NFE) AF: 0.0750 AC: 5089 AN: 67856

Other (OTH) AF: 0.138 AC: 290 AN: 2108

Alfa AF: 0.0975 Hom.: 753

Bravo AF: 0.161

Asia WGS AF: 0.0360 AC: 126 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	11
DANN	Benign	0.79
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10162417; hg19: chr14-22929700;