14-22370225-A-G

Variant names:

• chr14-22370225-A-G
• rs8014927

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 0.243 in 150,318 control chromosomes in the GnomAD database, including 4,632 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 0.24 (4632 hom., cov: 24)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557
• 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 (NFE) allele frequency at 95% confidence interval = 0.281 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+30819T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36524 AN: 150200 Hom.: 4631 Cov.: 24

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0800

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.243 AC: 36555 AN: 150318 Hom.: 4632 Cov.: 24 AF XY: 0.237 AC XY: 17408 AN XY: 73394

African (AFR) AF: 0.243 AC: 9901 AN: 40772

American (AMR) AF: 0.174 AC: 2596 AN: 14962

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 579 AN: 3452

East Asian (EAS) AF: 0.0798 AC: 409 AN: 5128

South Asian (SAS) AF: 0.136 AC: 647 AN: 4760

European-Finnish (FIN) AF: 0.241 AC: 2493 AN: 10330

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19209 AN: 67622

Other (OTH) AF: 0.230 AC: 480 AN: 2086

Alfa AF: 0.260 Hom.: 9178

Bravo AF: 0.238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs8014927; hg19: chr14-22838630;