14-22312080-C-T

Variant names:

• chr14-22312080-C-T
• rs3811259

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 0.241 in 150,674 control chromosomes in the GnomAD database, including 5,520 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 0.24 (5520 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22312080C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+88964G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36323 AN: 150556 Hom.: 5505 Cov.: 26

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.241 AC: 36339 AN: 150674 Hom.: 5520 Cov.: 26 AF XY: 0.252 AC XY: 18512 AN XY: 73494

African (AFR) AF: 0.0916 AC: 3757 AN: 41034

American (AMR) AF: 0.401 AC: 6023 AN: 15010

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3462

East Asian (EAS) AF: 0.609 AC: 3118 AN: 5120

South Asian (SAS) AF: 0.323 AC: 1526 AN: 4730

European-Finnish (FIN) AF: 0.330 AC: 3410 AN: 10344

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 16989 AN: 67680

Other (OTH) AF: 0.257 AC: 538 AN: 2094

Alfa AF: 0.248 Hom.: 8622

Bravo AF: 0.243

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.6
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs3811259; hg19: chr14-22780499;