7-142666251-A-G

Variant names:

• chr7-142666251-A-G
• rs4726556

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 0.127 in 168,298 control chromosomes in the GnomAD database, including 1,617 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 0.13 (1463 hom., cov: 29)
  • Exomes 𝑓: 0.12 (154 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 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: 0.127 AC: 19305 AN: 151674 Hom.: 1461 Cov.: 29

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.0991

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0839

Gnomad OTH AF: 0.124

GnomAD4 exome AF: 0.120 AC: 1986 AN: 16504 Hom.: 154 Cov.: 0 AF XY: 0.117 AC XY: 1033 AN XY: 8824

African (AFR) AF: 0.192 AC: 83 AN: 432

American (AMR) AF: 0.218 AC: 111 AN: 510

Ashkenazi Jewish (ASJ) AF: 0.0793 AC: 53 AN: 668

East Asian (EAS) AF: 0.283 AC: 420 AN: 1482

South Asian (SAS) AF: 0.0372 AC: 7 AN: 188

European-Finnish (FIN) AF: 0.111 AC: 146 AN: 1316

Middle Eastern (MID) AF: 0.125 AC: 10 AN: 80

European-Non Finnish (NFE) AF: 0.0953 AC: 1023 AN: 10730

Other (OTH) AF: 0.121 AC: 133 AN: 1098

GnomAD4 genome AF: 0.127 AC: 19345 AN: 151794 Hom.: 1463 Cov.: 29 AF XY: 0.128 AC XY: 9509 AN XY: 74192

African (AFR) AF: 0.185 AC: 7648 AN: 41332

American (AMR) AF: 0.180 AC: 2737 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0629 AC: 218 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1256 AN: 5150

South Asian (SAS) AF: 0.0728 AC: 350 AN: 4808

European-Finnish (FIN) AF: 0.0991 AC: 1047 AN: 10568

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0839 AC: 5698 AN: 67944

Other (OTH) AF: 0.123 AC: 258 AN: 2104

Alfa AF: 0.0848 Hom.: 148

Bravo AF: 0.139

Asia WGS AF: 0.162 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	7.5
DANN	Benign	0.60
PhyloP100		0.37
PromoterAI		0.0040	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;