rs10483273

chr14-22448054-A-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.225+33187T>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 0.0948 in 150,356 control chromosomes in the GnomAD database, including 769 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 0.095 (769 hom., cov: 25)
• Consequence: TRD-AS1 NR_148361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRD-AS1	NR_148361.1	n.225+33187T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.225+33187T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0947 AC: 14235 AN: 150238 Hom.: 766 Cov.: 25

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.0633

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0833

Gnomad FIN AF: 0.0861

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0739

Gnomad OTH AF: 0.0996

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

GnomAD4 genome AF: 0.0948 AC: 14256 AN: 150356 Hom.: 769 Cov.: 25 AF XY: 0.0962 AC XY: 7062 AN XY: 73408

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0633

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.0836

Gnomad4 FIN AF: 0.0861

Gnomad4 NFE AF: 0.0739

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0845 Hom.: 850

Bravo AF: 0.104

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	6.7
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483273; hg19: chr14-22917046;