rs2001022

Positions:

• chr14-22289383-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.271-88001G>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 0.0718 in 149,688 control chromosomes in the GnomAD database, including 457 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 0.072 (457 hom., cov: 26)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319

Genes affected

TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

LOC107984649 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984649	XR_001750634.2	n.205+369G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.271-88001G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0718 AC: 10735 AN: 149568 Hom.: 454 Cov.: 26

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0310

Gnomad AMR AF: 0.0589

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0319

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.0778

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

GnomAD4 genome AF: 0.0718 AC: 10747 AN: 149688 Hom.: 457 Cov.: 26 AF XY: 0.0705 AC XY: 5149 AN XY: 73008

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0588

Gnomad4 ASJ AF: 0.0700

Gnomad4 EAS AF: 0.0795

Gnomad4 SAS AF: 0.0571

Gnomad4 FIN AF: 0.0319

Gnomad4 NFE AF: 0.0594

Gnomad4 OTH AF: 0.0770

Alfa AF: 0.0519 Hom.: 135

Bravo AF: 0.0744

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.87
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2001022; hg19: chr14-22757266;