rs11157552

Variant names:

• chr14-22383427-T-C
• rs11157552

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 0.799 in 150,640 control chromosomes in the GnomAD database, including 48,643 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 0.80 (48643 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413
• 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 (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514473.2. 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
	TRD-AS1	NR_148361.1		n.226-1022A>G		intron	N/A
	TRD-AS1	NR_148362.1		n.290-1022A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000514473.2	TSL:2	n.226-1022A>G		intron	N/A
	TRD-AS1	ENST00000541008.6	TSL:4	n.277-1022A>G		intron	N/A
	TRD-AS1	ENST00000545670.5	TSL:4	n.276-1022A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.799 AC: 120197 AN: 150522 Hom.: 48593 Cov.: 25

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.799 AC: 120306 AN: 150640 Hom.: 48643 Cov.: 25 AF XY: 0.795 AC XY: 58417 AN XY: 73506

African (AFR) AF: 0.930 AC: 37988 AN: 40858

American (AMR) AF: 0.715 AC: 10751 AN: 15044

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2297 AN: 3462

East Asian (EAS) AF: 0.821 AC: 4235 AN: 5156

South Asian (SAS) AF: 0.814 AC: 3868 AN: 4754

European-Finnish (FIN) AF: 0.725 AC: 7505 AN: 10354

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51127 AN: 67732

Other (OTH) AF: 0.769 AC: 1598 AN: 2078

Alfa AF: 0.765 Hom.: 59076

Bravo AF: 0.803

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs11157552; hg19: chr14-22851830;