rs12891257

chr14-22393232-C-T

Variant summary

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

The NR_148361.1(TRD-AS1):n.226-10827G>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 0.0611 in 150,890 control chromosomes in the GnomAD database, including 396 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 0.061 (396 hom., cov: 25)
• Consequence: TRD-AS1 NR_148361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

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 (SAS) allele frequency at 95% confidence interval = 0.0958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRD-AS1	NR_148361.1	n.226-10827G>A		intron_variant, non_coding_transcript_variant
TRD-AS1	NR_148362.1	n.289+7812G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+7812G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0611 AC: 9213 AN: 150772 Hom.: 396 Cov.: 25

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.0597

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

GnomAD4 genome AF: 0.0611 AC: 9215 AN: 150890 Hom.: 396 Cov.: 25 AF XY: 0.0605 AC XY: 4457 AN XY: 73676

Gnomad4 AFR AF: 0.0162

Gnomad4 AMR AF: 0.0469

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.0586

Alfa AF: 0.0904 Hom.: 320

Bravo AF: 0.0552

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.3
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12891257; hg19: chr14-22861635;