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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRB		n.142759369G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;