rs4981422

Variant names:

• chr14-22329546-G-A
• rs4981422

Your query was ambiguous. Multiple possible variants found:

• chr14-22329546-G-A
• chr14-22329546-G-C
• chr14-22329546-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 0.554 in 150,586 control chromosomes in the GnomAD database, including 23,373 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 0.55 (23373 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 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+71498C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.554 AC: 83341 AN: 150468 Hom.: 23357 Cov.: 26

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.554 AC: 83396 AN: 150586 Hom.: 23373 Cov.: 26 AF XY: 0.553 AC XY: 40656 AN XY: 73504

African (AFR) AF: 0.550 AC: 22469 AN: 40864

American (AMR) AF: 0.452 AC: 6783 AN: 14998

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1652 AN: 3446

East Asian (EAS) AF: 0.645 AC: 3321 AN: 5152

South Asian (SAS) AF: 0.618 AC: 2944 AN: 4762

European-Finnish (FIN) AF: 0.580 AC: 6022 AN: 10382

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38505 AN: 67682

Other (OTH) AF: 0.526 AC: 1102 AN: 2096

Alfa AF: 0.550 Hom.: 34785

Bravo AF: 0.539

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.0
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs4981422; hg19: chr14-22797976;