rs11157596

Variant names:

• chr14-22438076-G-A
• rs11157596

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 0.576 in 149,854 control chromosomes in the GnomAD database, including 25,317 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 0.58 (25317 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• Publications: 2 publications found

Genes affected

TRA (HGNC:12027):

TRD (HGNC:12252):

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 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.225+43165C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000514473.2	TSL:2	n.225+43165C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.576 AC: 86300 AN: 149736 Hom.: 25286 Cov.: 25

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.576 AC: 86384 AN: 149854 Hom.: 25317 Cov.: 25 AF XY: 0.578 AC XY: 42255 AN XY: 73120

African (AFR) AF: 0.669 AC: 27166 AN: 40590

American (AMR) AF: 0.439 AC: 6527 AN: 14876

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2031 AN: 3446

East Asian (EAS) AF: 0.701 AC: 3602 AN: 5140

South Asian (SAS) AF: 0.680 AC: 3237 AN: 4762

European-Finnish (FIN) AF: 0.544 AC: 5530 AN: 10172

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36446 AN: 67596

Other (OTH) AF: 0.537 AC: 1117 AN: 2080

Alfa AF: 0.554 Hom.: 17382

Bravo AF: 0.565

Asia WGS AF: 0.694 AC: 2407 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.23
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs11157596; hg19: chr14-22907068;