rs1076549

Positions:

• chr14-22303409-T-C

Variant summary

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

The ENST00000656379.1(TRD-AS1):​n.270+97635A>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 0.848 in 151,122 control chromosomes in the GnomAD database, including 54,733 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 0.85 (54733 hom., cov: 25)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

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 (Cadd=4.289).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 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+97635A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128075 AN: 151004 Hom.: 54681 Cov.: 25

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.848 AC: 128184 AN: 151122 Hom.: 54733 Cov.: 25 AF XY: 0.851 AC XY: 62850 AN XY: 73876

Gnomad4 AFR AF: 0.948

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.847

Alfa AF: 0.801 Hom.: 52331

Bravo AF: 0.854

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1076549; hg19: -;