14-22293365-G-A

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656379.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000656379.1		n.271-91983C>T		intron	N/A

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 v4.9

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;