rs4981423

Variant names:

• chr14-22340329-G-A
• rs4981423

Your query was ambiguous. Multiple possible variants found:

• chr14-22340329-G-A
• chr14-22340329-G-C
• chr14-22340329-G-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 0.257 in 150,588 control chromosomes in the GnomAD database, including 5,145 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 0.26 (5145 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656379.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000656379.1		n.270+60715C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38600 AN: 150470 Hom.: 5142 Cov.: 25

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.257 AC: 38629 AN: 150588 Hom.: 5145 Cov.: 25 AF XY: 0.250 AC XY: 18376 AN XY: 73534

African (AFR) AF: 0.287 AC: 11702 AN: 40834

American (AMR) AF: 0.181 AC: 2724 AN: 15050

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 598 AN: 3458

East Asian (EAS) AF: 0.0820 AC: 422 AN: 5144

South Asian (SAS) AF: 0.135 AC: 645 AN: 4766

European-Finnish (FIN) AF: 0.244 AC: 2534 AN: 10378

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19257 AN: 67656

Other (OTH) AF: 0.240 AC: 505 AN: 2100

Alfa AF: 0.266 Hom.: 9332

Bravo AF: 0.253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.34
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs4981423; hg19: chr14-22808754;