rs2367486

Variant names:

• chr7-142784320-A-G
• rs2367486

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 0.498 in 151,582 control chromosomes in the GnomAD database, including 19,290 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 0.50 (19290 hom., cov: 28)
• Consequence: TRB intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 14 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.556 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: 0.499 AC: 75510 AN: 151466 Hom.: 19277 Cov.: 28

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.498 AC: 75563 AN: 151582 Hom.: 19290 Cov.: 28 AF XY: 0.496 AC XY: 36744 AN XY: 74066

African (AFR) AF: 0.465 AC: 19189 AN: 41252

American (AMR) AF: 0.566 AC: 8623 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1898 AN: 3464

East Asian (EAS) AF: 0.235 AC: 1212 AN: 5162

South Asian (SAS) AF: 0.286 AC: 1374 AN: 4812

European-Finnish (FIN) AF: 0.565 AC: 5926 AN: 10480

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35633 AN: 67876

Other (OTH) AF: 0.506 AC: 1065 AN: 2106

Alfa AF: 0.514 Hom.: 70554

Bravo AF: 0.503

Asia WGS AF: 0.273 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.5
DANN	Benign	0.46
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2367486; hg19: chr7-142492130;