rs10260647

Variant names:

• chr7-142665040-G-A
• rs10260647

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 0.184 in 151,474 control chromosomes in the GnomAD database, including 2,710 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 0.18 (2710 hom., cov: 28)
• Consequence: TRB intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 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: 0.184 AC: 27792 AN: 151356 Hom.: 2703 Cov.: 28

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.184 AC: 27844 AN: 151474 Hom.: 2710 Cov.: 28 AF XY: 0.183 AC XY: 13513 AN XY: 73992

African (AFR) AF: 0.215 AC: 8843 AN: 41226

American (AMR) AF: 0.214 AC: 3248 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3462

East Asian (EAS) AF: 0.239 AC: 1227 AN: 5140

South Asian (SAS) AF: 0.143 AC: 684 AN: 4784

European-Finnish (FIN) AF: 0.161 AC: 1689 AN: 10466

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11106 AN: 67896

Other (OTH) AF: 0.175 AC: 368 AN: 2108

Alfa AF: 0.170 Hom.: 3306

Bravo AF: 0.191

Asia WGS AF: 0.189 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.83
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs10260647; hg19: chr7-142372872;