chr14-22360462-A-G

Variant names:

• chr14-22360462-A-G
• rs2331662

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 0.11 in 150,472 control chromosomes in the GnomAD database, including 1,323 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 0.11 (1323 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000656379.1		n.270+40582T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16557 AN: 150354 Hom.: 1324 Cov.: 26

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0419

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0784

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0650

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.110 AC: 16548 AN: 150472 Hom.: 1323 Cov.: 26 AF XY: 0.114 AC XY: 8404 AN XY: 73494

African (AFR) AF: 0.145 AC: 5941 AN: 40882

American (AMR) AF: 0.108 AC: 1608 AN: 14894

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 286 AN: 3456

East Asian (EAS) AF: 0.439 AC: 2252 AN: 5130

South Asian (SAS) AF: 0.207 AC: 990 AN: 4774

European-Finnish (FIN) AF: 0.0784 AC: 811 AN: 10346

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0650 AC: 4398 AN: 67698

Other (OTH) AF: 0.0966 AC: 202 AN: 2092

Alfa AF: 0.0737 Hom.: 814

Bravo AF: 0.111

Asia WGS AF: 0.295 AC: 1024 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.39
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2331662; hg19: chr14-22828889;