rs11850894

Variant names:

• chr14-22312243-G-T
• rs11850894

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0553 in 150,856 control chromosomes in the GnomAD database, including 239 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 0.055 (239 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 4 publications found

Genes affected

TRA (HGNC:12027):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22312243G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+88801C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0553 AC: 8339 AN: 150738 Hom.: 237 Cov.: 26

Gnomad AFR AF: 0.0699

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0356

Gnomad ASJ AF: 0.0665

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0898

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0547

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0553 AC: 8346 AN: 150856 Hom.: 239 Cov.: 26 AF XY: 0.0549 AC XY: 4042 AN XY: 73620

African (AFR) AF: 0.0698 AC: 2859 AN: 40974

American (AMR) AF: 0.0355 AC: 534 AN: 15038

Ashkenazi Jewish (ASJ) AF: 0.0665 AC: 230 AN: 3460

East Asian (EAS) AF: 0.0103 AC: 53 AN: 5162

South Asian (SAS) AF: 0.0899 AC: 426 AN: 4738

European-Finnish (FIN) AF: 0.0394 AC: 410 AN: 10416

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0547 AC: 3709 AN: 67776

Other (OTH) AF: 0.0474 AC: 99 AN: 2090

Alfa AF: 0.0587 Hom.: 261

Bravo AF: 0.0545

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.74
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs11850894; hg19: chr14-22780662;