rs4981423

Positions:

• chr14-22340329-G-A
• chr14-22340329-G-C
• chr14-22340329-G-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+60715C>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 0.257 in 150,588 control chromosomes in the GnomAD database, including 5,145 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 0.26 (5145 hom., cov: 25)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

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 (AFR) allele frequency at 95% confidence interval = 0.282 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+60715C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38600 AN: 150470 Hom.: 5142 Cov.: 25

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.257 AC: 38629 AN: 150588 Hom.: 5145 Cov.: 25 AF XY: 0.250 AC XY: 18376 AN XY: 73534

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0820

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.240

Alfa AF: 0.265 Hom.: 7309

Bravo AF: 0.253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4981423; hg19: chr14-22808754;