rs1569297

chr14-22304710-T-C

Variant summary

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

The ENST00000656379.1(TRD-AS1):n.270+96334A>G 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 0.674 in 150,886 control chromosomes in the GnomAD database, including 36,189 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 0.67 (36189 hom., cov: 26)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476

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 (Cadd=12.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+96334A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.675 AC: 101738 AN: 150768 Hom.: 36187 Cov.: 26

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.674 AC: 101762 AN: 150886 Hom.: 36189 Cov.: 26 AF XY: 0.682 AC XY: 50271 AN XY: 73678

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.697

Alfa AF: 0.713 Hom.: 6675

Bravo AF: 0.659

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Cadd	Benign	13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1569297; hg19: -;