chr14-22471852-C-T

Variant names:

• chr14-22471852-C-T
• rs10483277

Variant summary

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

The variant allele was found at a frequency of 0.122 in 151,460 control chromosomes in the GnomAD database, including 1,318 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 (1318 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879

Genes affected

TRA (HGNC:12027):

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22471852C>T		intragenic_variant
TRD-AS1	NR_148361.1	n.225+9389G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.225+9389G>A		intron_variant	Intron 2 of 2	2
TRD-AS1	ENST00000556777.2	n.563-6566G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18427 AN: 151342 Hom.: 1320 Cov.: 26

Gnomad AFR AF: 0.0632

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0784

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.122 AC: 18430 AN: 151460 Hom.: 1318 Cov.: 26 AF XY: 0.118 AC XY: 8710 AN XY: 74046

Gnomad4 AFR AF: 0.0632

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0783

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.120

Alfa AF: 0.131 Hom.: 723

Bravo AF: 0.120

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483277; hg19: chr14-22940842;