14-22321205-G-A

Variant names:

• chr14-22321205-G-A
• rs8007403

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 0.476 in 150,816 control chromosomes in the GnomAD database, including 18,013 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 0.48 (18013 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000656379.1		n.270+79839C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.476 AC: 71795 AN: 150698 Hom.: 17997 Cov.: 26

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.476 AC: 71862 AN: 150816 Hom.: 18013 Cov.: 26 AF XY: 0.478 AC XY: 35227 AN XY: 73660

African (AFR) AF: 0.630 AC: 25781 AN: 40906

American (AMR) AF: 0.384 AC: 5787 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1576 AN: 3466

East Asian (EAS) AF: 0.566 AC: 2922 AN: 5160

South Asian (SAS) AF: 0.517 AC: 2472 AN: 4784

European-Finnish (FIN) AF: 0.450 AC: 4683 AN: 10408

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27191 AN: 67728

Other (OTH) AF: 0.472 AC: 989 AN: 2094

Alfa AF: 0.423 Hom.: 7754

Bravo AF: 0.475

Asia WGS AF: 0.559 AC: 1940 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.21
PhyloP100		0.082

Splicing

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

Other links and lift over

dbSNP: rs8007403; hg19: chr14-22789637;