7-142499594-T-C

Position:

• chr7-142499594-T-C

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.142499594T>C		intergenic_region
TRB		n.142499594T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0638

Gnomad4 EAS AF: 0.0694

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.0585

Gnomad4 NFE AF: 0.0740

Gnomad4 OTH AF: 0.166

Alfa AF: 0.102 Hom.: 761

Bravo AF: 0.175

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10480340; hg19: chr7-142132352;