rs3811222

chr14-22482025-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_148361.1(TRD-AS1):n.108-667C>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 0.122 in 151,330 control chromosomes in the GnomAD database, including 1,593 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 0.12 (1593 hom., cov: 27)
• Consequence: TRD-AS1 NR_148361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRD-AS1	NR_148361.1	n.108-667C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.108-667C>T		intron_variant, non_coding_transcript_variant		2
TRD-AS1	ENST00000556777.2	n.445-667C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18512 AN: 151212 Hom.: 1593 Cov.: 27

Gnomad AFR AF: 0.0832

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.122 AC: 18514 AN: 151330 Hom.: 1593 Cov.: 27 AF XY: 0.128 AC XY: 9448 AN XY: 73934

Gnomad4 AFR AF: 0.0834

Gnomad4 AMR AF: 0.0801

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.103

Alfa AF: 0.118 Hom.: 610

Bravo AF: 0.113

Asia WGS AF: 0.327 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.028
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3811222; hg19: chr14-22951014; COSMIC: COSV66607189;