7-142357119-C-T

Variant names:

• chr7-142357119-C-T
• rs2854536

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 0.404 in 151,930 control chromosomes in the GnomAD database, including 13,613 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 0.40 (13613 hom., cov: 31)
• Consequence: TRB intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445
• Publications: 9 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61361 AN: 151814 Hom.: 13609 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.404 AC: 61398 AN: 151930 Hom.: 13613 Cov.: 31 AF XY: 0.413 AC XY: 30649 AN XY: 74284

African (AFR) AF: 0.505 AC: 20908 AN: 41416

American (AMR) AF: 0.478 AC: 7288 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1230 AN: 3466

East Asian (EAS) AF: 0.763 AC: 3939 AN: 5160

South Asian (SAS) AF: 0.655 AC: 3154 AN: 4818

European-Finnish (FIN) AF: 0.309 AC: 3261 AN: 10570

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20346 AN: 67926

Other (OTH) AF: 0.429 AC: 905 AN: 2112

Alfa AF: 0.357 Hom.: 18654

Bravo AF: 0.420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.30
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2854536; hg19: chr7-142274854;