14-22319109-C-T

Variant names:

• chr14-22319109-C-T
• rs10047935

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 0.408 in 150,464 control chromosomes in the GnomAD database, including 12,980 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 0.41 (12980 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 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+81935G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61287 AN: 150346 Hom.: 12972 Cov.: 26

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.408 AC: 61336 AN: 150464 Hom.: 12980 Cov.: 26 AF XY: 0.414 AC XY: 30399 AN XY: 73456

African (AFR) AF: 0.486 AC: 19835 AN: 40786

American (AMR) AF: 0.352 AC: 5279 AN: 14994

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1512 AN: 3466

East Asian (EAS) AF: 0.563 AC: 2902 AN: 5152

South Asian (SAS) AF: 0.505 AC: 2395 AN: 4744

European-Finnish (FIN) AF: 0.426 AC: 4402 AN: 10324

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

European-Non Finnish (NFE) AF: 0.352 AC: 23803 AN: 67702

Other (OTH) AF: 0.417 AC: 874 AN: 2094

Alfa AF: 0.372 Hom.: 47064

Bravo AF: 0.402

Asia WGS AF: 0.542 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.3
DANN	Benign	0.76
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs10047935; hg19: chr14-22787541;