rs1540268

Positions:

• chr14-22307060-C-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+93984G>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 0.692 in 146,524 control chromosomes in the GnomAD database, including 36,019 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 0.69 (36019 hom., cov: 25)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 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+93984G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.692 AC: 101341 AN: 146408 Hom.: 36015 Cov.: 25

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.692 AC: 101367 AN: 146524 Hom.: 36019 Cov.: 25 AF XY: 0.699 AC XY: 50076 AN XY: 71684

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.707

Alfa AF: 0.743 Hom.: 87043

Bravo AF: 0.657

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1540268; hg19: chr14-22775479;