rs2213212

Variant names:

• chr7-142698925-A-C
• rs2213212

Your query was ambiguous. Multiple possible variants found:

• chr7-142698925-A-C
• chr7-142698925-A-G
• chr7-142698925-A-T

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;