7-142698925-A-C

Variant names:

• chr7-142698925-A-C
• rs2213212

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 0.634 in 151,026 control chromosomes in the GnomAD database, including 30,762 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 0.63 (30762 hom., cov: 27)
• Consequence: TRB intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 5 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRB		n.142698925A>C		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.634 AC: 95630 AN: 150908 Hom.: 30724 Cov.: 27

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.634 AC: 95726 AN: 151026 Hom.: 30762 Cov.: 27 AF XY: 0.640 AC XY: 47209 AN XY: 73782

African (AFR) AF: 0.554 AC: 22721 AN: 41016

American (AMR) AF: 0.666 AC: 10078 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2083 AN: 3462

East Asian (EAS) AF: 0.889 AC: 4563 AN: 5130

South Asian (SAS) AF: 0.702 AC: 3340 AN: 4756

European-Finnish (FIN) AF: 0.739 AC: 7743 AN: 10474

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43145 AN: 67768

Other (OTH) AF: 0.630 AC: 1317 AN: 2090

Alfa AF: 0.634 Hom.: 15448

Bravo AF: 0.624

Asia WGS AF: 0.808 AC: 2806 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2213212; hg19: chr7-142406737;