14-22288387-T-C

Variant names:

• chr14-22288387-T-C
• rs10129606

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 0.371 in 148,588 control chromosomes in the GnomAD database, including 10,593 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 0.37 (10593 hom., cov: 23)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

Genes affected

TRA (HGNC:12027):

TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

LOC107984649 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22288387T>C		intragenic_variant
LOC107984649	XR_001750634.2	n.206-1193A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.271-87005A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.371 AC: 55127 AN: 148470 Hom.: 10576 Cov.: 23

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.371 AC: 55196 AN: 148588 Hom.: 10593 Cov.: 23 AF XY: 0.366 AC XY: 26464 AN XY: 72404

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.373

Alfa AF: 0.349 Hom.: 18003

Bravo AF: 0.375

Asia WGS AF: 0.272 AC: 944 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10129606; hg19: chr14-22756270;