rs11850894

chr14-22312243-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+88801C>A 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 0.0553 in 150,856 control chromosomes in the GnomAD database, including 239 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 0.055 (239 hom., cov: 26)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0829 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+88801C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0553 AC: 8339 AN: 150738 Hom.: 237 Cov.: 26

Gnomad AFR AF: 0.0699

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0356

Gnomad ASJ AF: 0.0665

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0898

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0547

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0553 AC: 8346 AN: 150856 Hom.: 239 Cov.: 26 AF XY: 0.0549 AC XY: 4042 AN XY: 73620

Gnomad4 AFR AF: 0.0698

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.0665

Gnomad4 EAS AF: 0.0103

Gnomad4 SAS AF: 0.0899

Gnomad4 FIN AF: 0.0394

Gnomad4 NFE AF: 0.0547

Gnomad4 OTH AF: 0.0474

Alfa AF: 0.0603 Hom.: 139

Bravo AF: 0.0545

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.6
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11850894; hg19: chr14-22780662;