rs10162417

chr14-22460708-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.225+20533A>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 0.147 in 151,030 control chromosomes in the GnomAD database, including 2,781 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 0.15 (2781 hom., cov: 26)
• Consequence: TRD-AS1 NR_148361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

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=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRD-AS1	NR_148361.1	n.225+20533A>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+20533A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22244 AN: 150912 Hom.: 2775 Cov.: 26

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.0518

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0984

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0750

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.147 AC: 22272 AN: 151030 Hom.: 2781 Cov.: 26 AF XY: 0.144 AC XY: 10635 AN XY: 73816

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0984

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.0624

Gnomad4 NFE AF: 0.0750

Gnomad4 OTH AF: 0.138

Alfa AF: 0.0966 Hom.: 676

Bravo AF: 0.161

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	11
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10162417; hg19: chr14-22929700;