7-142499594-T-C

Variant names:

• chr7-142499594-T-C
• rs10480340

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 0.182 in 136,216 control chromosomes in the GnomAD database, including 3,601 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 0.18 (3601 hom., cov: 32)
• Consequence: TRB intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.182 AC: 24703 AN: 136102 Hom.: 3590 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.0958

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0638

Gnomad EAS AF: 0.0693

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0740

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.182 AC: 24753 AN: 136216 Hom.: 3601 Cov.: 32 AF XY: 0.180 AC XY: 11933 AN XY: 66440

African (AFR) AF: 0.413 AC: 16453 AN: 39826

American (AMR) AF: 0.116 AC: 1564 AN: 13524

Ashkenazi Jewish (ASJ) AF: 0.0638 AC: 192 AN: 3008

East Asian (EAS) AF: 0.0694 AC: 302 AN: 4350

South Asian (SAS) AF: 0.211 AC: 877 AN: 4148

European-Finnish (FIN) AF: 0.0585 AC: 514 AN: 8792

Middle Eastern (MID) AF: 0.197 AC: 48 AN: 244

European-Non Finnish (NFE) AF: 0.0740 AC: 4416 AN: 59656

Other (OTH) AF: 0.166 AC: 310 AN: 1864

Alfa AF: 0.106 Hom.: 1170

Bravo AF: 0.175

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10480340; hg19: chr7-142132352;