chr7-142666251-A-C

Variant names:

• chr7-142666251-A-C
• rs4726556

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 29)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TRB intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• Publications: 1 publications found

Genes affected

TRB (HGNC:12155):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRB		n.142666251A>C		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 16554 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8846

African (AFR) AF: 0.00 AC: 0 AN: 432

American (AMR) AF: 0.00 AC: 0 AN: 512

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 670

East Asian (EAS) AF: 0.00 AC: 0 AN: 1490

South Asian (SAS) AF: 0.00 AC: 0 AN: 190

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1318

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 80

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 10758

Other (OTH) AF: 0.00 AC: 0 AN: 1104

GnomAD4 genome Cov.: 29

Alfa AF: 0.00 Hom.: 148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	6.7
DANN	Benign	0.56
PhyloP100		0.37
PromoterAI		0.0064	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4726556; hg19: chr7-142374083;