14-22391078-T-G

Variant summary

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

The NR_148361.1(TRD-AS1):n.226-8673A>C 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 0.34 in 150,016 control chromosomes in the GnomAD database, including 9,060 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 0.34 (9060 hom., cov: 25)
• Consequence: TRD-AS1 NR_148361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRD-AS1	NR_148361.1	n.226-8673A>C		intron_variant, non_coding_transcript_variant
TRD-AS1	NR_148362.1	n.290-8673A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+9966A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.340 AC: 50918 AN: 149896 Hom.: 9052 Cov.: 25

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.0886

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.343

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.340 AC: 50939 AN: 150016 Hom.: 9060 Cov.: 25 AF XY: 0.330 AC XY: 24160 AN XY: 73216

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.0884

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.323

Alfa AF: 0.351 Hom.: 19345

Bravo AF: 0.337

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3811244; hg19: chr14-22859482;