rs4981422

chr14-22329546-G-Achr14-22329546-G-Cchr14-22329546-G-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+71498C>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 0.554 in 150,586 control chromosomes in the GnomAD database, including 23,373 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 0.55 (23373 hom., cov: 26)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 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+71498C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.554 AC: 83341 AN: 150468 Hom.: 23357 Cov.: 26

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.554 AC: 83396 AN: 150586 Hom.: 23373 Cov.: 26 AF XY: 0.553 AC XY: 40656 AN XY: 73504

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.526

Alfa AF: 0.551 Hom.: 27461

Bravo AF: 0.539

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	6.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4981422; hg19: chr14-22797976;