14-22321205-G-A

Position:

• chr14-22321205-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656379.1(TRD-AS1):​n.270+79839C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

Genes affected

TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+79839C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.472

Alfa AF: 0.422 Hom.: 6946

Bravo AF: 0.475

Asia WGS AF: 0.559 AC: 1940 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8007403; hg19: chr14-22789637;