rs13230029

Variant names:

• chr7-142759369-G-C
• rs13230029

Your query was ambiguous. Multiple possible variants found:

• chr7-142759369-G-C
• chr7-142759369-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 0.538 in 144,584 control chromosomes in the GnomAD database, including 17,934 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 0.54 (17934 hom., cov: 33)
• Consequence: TRB intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 5 publications found

Genes affected

TRB (HGNC:12155):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.538 AC: 77752 AN: 144474 Hom.: 17931 Cov.: 33

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.461

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.538 AC: 77809 AN: 144584 Hom.: 17934 Cov.: 33 AF XY: 0.534 AC XY: 37832 AN XY: 70820

African (AFR) AF: 0.479 AC: 16621 AN: 34732

American (AMR) AF: 0.581 AC: 8656 AN: 14898

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2049 AN: 3462

East Asian (EAS) AF: 0.241 AC: 1241 AN: 5160

South Asian (SAS) AF: 0.345 AC: 1649 AN: 4780

European-Finnish (FIN) AF: 0.615 AC: 6467 AN: 10524

Middle Eastern (MID) AF: 0.462 AC: 133 AN: 288

European-Non Finnish (NFE) AF: 0.581 AC: 39401 AN: 67824

Other (OTH) AF: 0.540 AC: 1084 AN: 2008

Alfa AF: 0.529 Hom.: 1418

Asia WGS AF: 0.273 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.17
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs13230029; hg19: chr7-142467216;