14-22470475-A-C

Position:

• chr14-22470475-A-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+10766T>G 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 0.427 in 150,330 control chromosomes in the GnomAD database, including 14,144 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 0.43 (14144 hom., cov: 25)
• Consequence: TRD-AS1 NR_148361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRD-AS1	NR_148361.1	n.225+10766T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.225+10766T>G		intron_variant, non_coding_transcript_variant		2
TRD-AS1	ENST00000556777.2	n.563-5189T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64123 AN: 150212 Hom.: 14133 Cov.: 25

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.427 AC: 64156 AN: 150330 Hom.: 14144 Cov.: 25 AF XY: 0.426 AC XY: 31272 AN XY: 73438

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.401

Alfa AF: 0.388 Hom.: 5721

Bravo AF: 0.432

Asia WGS AF: 0.447 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8020193; hg19: chr14-22939467;