rs8020193

Variant names:

• chr14-22470475-A-C
• rs8020193

Your query was ambiguous. Multiple possible variants found:

• chr14-22470475-A-C
• chr14-22470475-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 0.427 in 150,330 control chromosomes in the GnomAD database, including 14,144 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 0.43 (14144 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22470475A>C		intragenic_variant
TRD-AS1	NR_148361.1	n.225+10766T>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.225+10766T>G		intron_variant	Intron 2 of 2	2
TRD-AS1	ENST00000556777.2	n.563-5189T>G		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64123 AN: 150212 Hom.: 14133 Cov.: 25

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.427 AC: 64156 AN: 150330 Hom.: 14144 Cov.: 25 AF XY: 0.426 AC XY: 31272 AN XY: 73438

African (AFR) AF: 0.547 AC: 22243 AN: 40644

American (AMR) AF: 0.366 AC: 5497 AN: 15024

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1338 AN: 3438

East Asian (EAS) AF: 0.522 AC: 2681 AN: 5140

South Asian (SAS) AF: 0.389 AC: 1849 AN: 4756

European-Finnish (FIN) AF: 0.343 AC: 3562 AN: 10392

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25576 AN: 67652

Other (OTH) AF: 0.401 AC: 838 AN: 2088

Alfa AF: 0.393 Hom.: 8540

Bravo AF: 0.432

Asia WGS AF: 0.447 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs8020193; hg19: chr14-22939467;