rs1882704

Positions:

• chr14-22456360-G-A
• chr14-22456360-G-C

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+24881C>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 0.764 in 150,458 control chromosomes in the GnomAD database, including 44,124 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 0.76 (44124 hom., cov: 25)
• Consequence: TRD-AS1 NR_148361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRD-AS1	NR_148361.1	n.225+24881C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.225+24881C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.764 AC: 114858 AN: 150340 Hom.: 44078 Cov.: 25

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.764 AC: 114966 AN: 150458 Hom.: 44124 Cov.: 25 AF XY: 0.765 AC XY: 56211 AN XY: 73440

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.744

Alfa AF: 0.734 Hom.: 82391

Bravo AF: 0.767

Asia WGS AF: 0.814 AC: 2831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.34
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1882704; hg19: chr14-22925352;