rs4435168

Positions:

• chr14-22281859-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.271-80477A>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 0.102 in 710,752 control chromosomes in the GnomAD database, including 4,395 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 0.081 (648 hom., cov: 25)
  • Exomes 𝑓: 0.11 (3747 hom.)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.164 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.271-80477A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0813 AC: 12221 AN: 150302 Hom.: 644 Cov.: 25

Gnomad AFR AF: 0.0206

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0843

Gnomad EAS AF: 0.0751

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0852

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0979

GnomAD3 exomes AF: 0.116 AC: 18020 AN: 154860 Hom.: 1207 AF XY: 0.119 AC XY: 10031 AN XY: 84574

Gnomad AFR exome AF: 0.0214

Gnomad AMR exome AF: 0.164

Gnomad ASJ exome AF: 0.0934

Gnomad EAS exome AF: 0.0822

Gnomad SAS exome AF: 0.173

Gnomad FIN exome AF: 0.0841

Gnomad NFE exome AF: 0.106

Gnomad OTH exome AF: 0.113

GnomAD4 exome AF: 0.108 AC: 60357 AN: 560332 Hom.: 3747 Cov.: 0 AF XY: 0.111 AC XY: 33892 AN XY: 304934

Gnomad4 AFR exome AF: 0.0224

Gnomad4 AMR exome AF: 0.161

Gnomad4 ASJ exome AF: 0.0899

Gnomad4 EAS exome AF: 0.0647

Gnomad4 SAS exome AF: 0.170

Gnomad4 FIN exome AF: 0.0913

Gnomad4 NFE exome AF: 0.102

Gnomad4 OTH exome AF: 0.103

GnomAD4 genome AF: 0.0814 AC: 12239 AN: 150420 Hom.: 648 Cov.: 25 AF XY: 0.0816 AC XY: 5992 AN XY: 73428

Gnomad4 AFR AF: 0.0205

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0843

Gnomad4 EAS AF: 0.0758

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0852

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0988

Alfa AF: 0.104 Hom.: 1224

Bravo AF: 0.0821

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4435168; hg19: chr14-22749742;