rs11157596

chr14-22438076-G-A

Variant summary

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

The NR_148361.1(TRD-AS1):n.225+43165C>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 0.576 in 149,854 control chromosomes in the GnomAD database, including 25,317 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 0.58 (25317 hom., cov: 25)
• Consequence: TRD-AS1 NR_148361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRD-AS1	NR_148361.1	n.225+43165C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.225+43165C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.576 AC: 86300 AN: 149736 Hom.: 25286 Cov.: 25

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.576 AC: 86384 AN: 149854 Hom.: 25317 Cov.: 25 AF XY: 0.578 AC XY: 42255 AN XY: 73120

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.537

Alfa AF: 0.554 Hom.: 14314

Bravo AF: 0.565

Asia WGS AF: 0.694 AC: 2407 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.1
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11157596; hg19: chr14-22907068;