chr14-22311424-A-G

Position:

• chr14-22311424-A-G

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 0.486 in 150,620 control chromosomes in the GnomAD database, including 18,780 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 0.49 (18780 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

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 (Cadd=7.903).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRA		n.22311424A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+89620T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73226 AN: 150502 Hom.: 18773 Cov.: 26

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.486 AC: 73245 AN: 150620 Hom.: 18780 Cov.: 26 AF XY: 0.491 AC XY: 36100 AN XY: 73564

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.509

Alfa AF: 0.527 Hom.: 25515

Bravo AF: 0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	7.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7146411; hg19: -;