rs916048

Positions:

• chr14-22322488-C-A
• chr14-22322488-C-G
• chr14-22322488-C-T

Variant summary

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

The ENST00000656379.1(TRD-AS1):​n.270+78556G>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 0.391 in 150,178 control chromosomes in the GnomAD database, including 11,659 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 0.39 (11659 hom., cov: 25)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 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+78556G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.391 AC: 58699 AN: 150060 Hom.: 11659 Cov.: 25

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.391 AC: 58732 AN: 150178 Hom.: 11659 Cov.: 25 AF XY: 0.396 AC XY: 29047 AN XY: 73296

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.387

Alfa AF: 0.360 Hom.: 5687

Bravo AF: 0.384

Asia WGS AF: 0.503 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.67
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs916048; hg19: chr14-22790920;