14-22434470-A-G

Position:

• chr14-22434470-A-G

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+46771T>C 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 0.444 in 150,360 control chromosomes in the GnomAD database, including 15,545 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 0.44 (15545 hom., cov: 25)
• Consequence: TRD-AS1 NR_148361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.792

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRD-AS1	NR_148361.1	n.225+46771T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.225+46771T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.444 AC: 66697 AN: 150242 Hom.: 15547 Cov.: 25

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.444 AC: 66720 AN: 150360 Hom.: 15545 Cov.: 25 AF XY: 0.448 AC XY: 32915 AN XY: 73434

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.420

Alfa AF: 0.479 Hom.: 24590

Bravo AF: 0.423

Asia WGS AF: 0.647 AC: 2248 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2141988; hg19: chr14-22903462;