rs3811260

Variant names:

• chr14-22300879-T-C
• rs3811260

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 0.0819 in 150,822 control chromosomes in the GnomAD database, including 844 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 0.082 (844 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22300879T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.271-99497A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12305 AN: 150708 Hom.: 834 Cov.: 26

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0276

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0810

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0494

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.0824

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

GnomAD4 genome AF: 0.0819 AC: 12359 AN: 150822 Hom.: 844 Cov.: 26 AF XY: 0.0806 AC XY: 5936 AN XY: 73670

African (AFR) AF: 0.188 AC: 7665 AN: 40842

American (AMR) AF: 0.0492 AC: 741 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.0810 AC: 280 AN: 3458

East Asian (EAS) AF: 0.135 AC: 694 AN: 5152

South Asian (SAS) AF: 0.0488 AC: 233 AN: 4772

European-Finnish (FIN) AF: 0.0223 AC: 233 AN: 10444

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0336 AC: 2279 AN: 67788

Other (OTH) AF: 0.0844 AC: 177 AN: 2096

Alfa AF: 0.0482 Hom.: 158

Bravo AF: 0.0896

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.40
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs3811260; hg19: chr14-22768770;