rs1474477

Positions:

• chr14-22317783-C-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+83261G>A 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 0.15 in 149,900 control chromosomes in the GnomAD database, including 1,743 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 (1743 hom., cov: 25)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 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+83261G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22402 AN: 149782 Hom.: 1740 Cov.: 25

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.0954

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.150 AC: 22418 AN: 149900 Hom.: 1743 Cov.: 25 AF XY: 0.151 AC XY: 11020 AN XY: 73134

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.0954

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.154

Alfa AF: 0.148 Hom.: 1001

Bravo AF: 0.159

Asia WGS AF: 0.162 AC: 563 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1474477; hg19: chr14-22786215;