rs12436199

Variant names:

• chr14-22348733-A-G
• rs12436199

Your query was ambiguous. Multiple possible variants found:

• chr14-22348733-A-G
• chr14-22348733-A-T

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 0.782 in 150,760 control chromosomes in the GnomAD database, including 46,347 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 0.78 (46347 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22348733A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+52311T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.782 AC: 117732 AN: 150642 Hom.: 46305 Cov.: 25

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.782 AC: 117832 AN: 150760 Hom.: 46347 Cov.: 25 AF XY: 0.779 AC XY: 57302 AN XY: 73562

African (AFR) AF: 0.867 AC: 35491 AN: 40946

American (AMR) AF: 0.709 AC: 10652 AN: 15028

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2293 AN: 3458

East Asian (EAS) AF: 0.822 AC: 4236 AN: 5156

South Asian (SAS) AF: 0.812 AC: 3866 AN: 4762

European-Finnish (FIN) AF: 0.731 AC: 7558 AN: 10338

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51220 AN: 67778

Other (OTH) AF: 0.755 AC: 1582 AN: 2096

Alfa AF: 0.756 Hom.: 28891

Bravo AF: 0.783

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs12436199; hg19: chr14-22817156;