rs10873018

Variant names:

• chr14-22445002-G-A
• rs10873018

Your query was ambiguous. Multiple possible variants found:

• chr14-22445002-G-A
• chr14-22445002-G-C

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 0.519 in 149,670 control chromosomes in the GnomAD database, including 20,432 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 0.52 (20432 hom., cov: 24)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22445002G>A		intragenic_variant
TRD		n.22445002G>A		intragenic_variant
TRD-AS1	NR_148361.1	n.225+36239C>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+36239C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.519 AC: 77631 AN: 149552 Hom.: 20425 Cov.: 24

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.519 AC: 77684 AN: 149670 Hom.: 20432 Cov.: 24 AF XY: 0.522 AC XY: 38141 AN XY: 73030

African (AFR) AF: 0.543 AC: 21971 AN: 40438

American (AMR) AF: 0.402 AC: 5955 AN: 14814

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1901 AN: 3442

East Asian (EAS) AF: 0.701 AC: 3599 AN: 5134

South Asian (SAS) AF: 0.660 AC: 3110 AN: 4710

European-Finnish (FIN) AF: 0.519 AC: 5342 AN: 10290

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.505 AC: 34098 AN: 67556

Other (OTH) AF: 0.481 AC: 1004 AN: 2088

Alfa AF: 0.497 Hom.: 25392

Bravo AF: 0.506

Asia WGS AF: 0.672 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.71
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10873018; hg19: chr14-22913994;