rs928916

Variant names:

• chr7-142565684-C-T
• rs928916

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 0.466 in 151,544 control chromosomes in the GnomAD database, including 17,385 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 0.47 (17385 hom., cov: 28)
• Consequence: TRB intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• 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 (Cadd=0.699).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 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: 0.467 AC: 70641 AN: 151424 Hom.: 17388 Cov.: 28

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.466 AC: 70662 AN: 151544 Hom.: 17385 Cov.: 28 AF XY: 0.469 AC XY: 34735 AN XY: 74044

African (AFR) AF: 0.330 AC: 13600 AN: 41244

American (AMR) AF: 0.356 AC: 5421 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1733 AN: 3468

East Asian (EAS) AF: 0.617 AC: 3174 AN: 5146

South Asian (SAS) AF: 0.463 AC: 2223 AN: 4802

European-Finnish (FIN) AF: 0.652 AC: 6822 AN: 10468

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36238 AN: 67904

Other (OTH) AF: 0.461 AC: 969 AN: 2102

Alfa AF: 0.498 Hom.: 3063

Bravo AF: 0.437

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.70
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs928916;