rs11157552

Positions:

• chr14-22383427-T-C

Variant summary

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

The NR_148361.1(TRD-AS1):​n.226-1022A>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 0.799 in 150,640 control chromosomes in the GnomAD database, including 48,643 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 0.80 (48643 hom., cov: 25)
• Consequence: TRD-AS1 NR_148361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRD-AS1	NR_148361.1	n.226-1022A>G		intron_variant, non_coding_transcript_variant
TRD-AS1	NR_148362.1	n.290-1022A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+17617A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.799 AC: 120197 AN: 150522 Hom.: 48593 Cov.: 25

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.799 AC: 120306 AN: 150640 Hom.: 48643 Cov.: 25 AF XY: 0.795 AC XY: 58417 AN XY: 73506

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.769

Alfa AF: 0.759 Hom.: 44912

Bravo AF: 0.803

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11157552; hg19: chr14-22851830;