rs10483271

Variant names:

• chr14-22293365-G-A
• rs10483271

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 0.281 in 151,094 control chromosomes in the GnomAD database, including 6,417 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 0.28 (6417 hom., cov: 27)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 3 publications found

Genes affected

TRA (HGNC:12027):

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22293365G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.271-91983C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42465 AN: 150976 Hom.: 6405 Cov.: 27

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.281 AC: 42513 AN: 151094 Hom.: 6417 Cov.: 27 AF XY: 0.276 AC XY: 20326 AN XY: 73770

African (AFR) AF: 0.383 AC: 15708 AN: 41024

American (AMR) AF: 0.198 AC: 2996 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 793 AN: 3462

East Asian (EAS) AF: 0.115 AC: 593 AN: 5164

South Asian (SAS) AF: 0.196 AC: 939 AN: 4788

European-Finnish (FIN) AF: 0.250 AC: 2618 AN: 10452

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18097 AN: 67802

Other (OTH) AF: 0.268 AC: 562 AN: 2098

Alfa AF: 0.283 Hom.: 5203

Bravo AF: 0.279

Asia WGS AF: 0.165 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.48
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10483271; hg19: chr14-22761250;