chr14-22289383-C-T

Variant names:

• chr14-22289383-C-T
• rs2001022

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 0.0718 in 149,688 control chromosomes in the GnomAD database, including 457 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 0.072 (457 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319
• Publications: 5 publications found

Genes affected

TRA (HGNC:12027):

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

LOC107984649 (HGNC:):

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 = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22289383C>T		intragenic_variant
LOC107984649	XR_001750634.2	n.205+369G>A		intron_variant	Intron 2 of 2
LOC107984649	XR_007064070.1	n.*210G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.271-88001G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0718 AC: 10735 AN: 149568 Hom.: 454 Cov.: 26

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0310

Gnomad AMR AF: 0.0589

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0319

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.0778

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

GnomAD4 genome AF: 0.0718 AC: 10747 AN: 149688 Hom.: 457 Cov.: 26 AF XY: 0.0705 AC XY: 5149 AN XY: 73008

African (AFR) AF: 0.108 AC: 4399 AN: 40562

American (AMR) AF: 0.0588 AC: 878 AN: 14930

Ashkenazi Jewish (ASJ) AF: 0.0700 AC: 242 AN: 3458

East Asian (EAS) AF: 0.0795 AC: 410 AN: 5158

South Asian (SAS) AF: 0.0571 AC: 271 AN: 4746

European-Finnish (FIN) AF: 0.0319 AC: 320 AN: 10032

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.0594 AC: 4009 AN: 67530

Other (OTH) AF: 0.0770 AC: 160 AN: 2078

Alfa AF: 0.0536 Hom.: 214

Bravo AF: 0.0744

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.87
DANN	Benign	0.44
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2001022; hg19: chr14-22757266;