rs17118064

chr14-22457498-G-Achr14-22457498-G-Cchr14-22457498-G-T

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+23743C>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 0.087 in 150,942 control chromosomes in the GnomAD database, including 679 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 0.087 (679 hom., cov: 25)
• Consequence: TRD-AS1 NR_148361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRD-AS1	NR_148361.1	n.225+23743C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.225+23743C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13127 AN: 150824 Hom.: 677 Cov.: 25

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0252

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0732

Gnomad OTH AF: 0.0921

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

GnomAD4 genome AF: 0.0870 AC: 13133 AN: 150942 Hom.: 679 Cov.: 25 AF XY: 0.0856 AC XY: 6309 AN XY: 73694

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.0768

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0246

Gnomad4 FIN AF: 0.0624

Gnomad4 NFE AF: 0.0732

Gnomad4 OTH AF: 0.0916

Alfa AF: 0.0621 Hom.: 164

Bravo AF: 0.0911

Asia WGS AF: 0.0220 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.97
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17118064; hg19: chr14-22926490;