rs7146411

Variant names:

• chr14-22311424-A-G
• rs7146411

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 0.486 in 150,620 control chromosomes in the GnomAD database, including 18,780 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 0.49 (18780 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 4 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 (Cadd=7.903).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000656379.1		n.270+89620T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73226 AN: 150502 Hom.: 18773 Cov.: 26

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.486 AC: 73245 AN: 150620 Hom.: 18780 Cov.: 26 AF XY: 0.491 AC XY: 36100 AN XY: 73564

African (AFR) AF: 0.323 AC: 13237 AN: 40994

American (AMR) AF: 0.591 AC: 8901 AN: 15058

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1545 AN: 3440

East Asian (EAS) AF: 0.738 AC: 3781 AN: 5122

South Asian (SAS) AF: 0.560 AC: 2670 AN: 4764

European-Finnish (FIN) AF: 0.522 AC: 5428 AN: 10390

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36123 AN: 67558

Other (OTH) AF: 0.509 AC: 1073 AN: 2106

Alfa AF: 0.525 Hom.: 32862

Bravo AF: 0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	7.9
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7146411;