rs227860

chr14-22481502-T-Achr14-22481502-T-G

Variant summary

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

The NR_148361.1(TRD-AS1):n.108-144A>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 0.134 in 151,656 control chromosomes in the GnomAD database, including 1,815 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 0.13 (1815 hom., cov: 27)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TRD-AS1 NR_148361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.967

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRD-AS1	NR_148361.1	n.108-144A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.108-144A>T		intron_variant, non_coding_transcript_variant		2
TRD-AS1	ENST00000556777.2	n.445-144A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20352 AN: 151538 Hom.: 1813 Cov.: 27

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.119

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.134 AC: 20348 AN: 151656 Hom.: 1815 Cov.: 27 AF XY: 0.139 AC XY: 10271 AN XY: 74102

Gnomad4 AFR AF: 0.0950

Gnomad4 AMR AF: 0.0955

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0586 Hom.: 62

Bravo AF: 0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	9.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs227860; hg19: chr14-22950491;