rs7782269

Variant names:

• chr7-38278989-A-G
• rs7782269

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 0.422 in 149,946 control chromosomes in the GnomAD database, including 14,248 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 0.42 (14248 hom., cov: 25)
• Consequence: TRG intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 6 publications found

Genes affected

TRG (HGNC:12271):

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 (AFR) allele frequency at 95% confidence interval = 0.576 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: 0.422 AC: 63157 AN: 149828 Hom.: 14224 Cov.: 25

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.422 AC: 63230 AN: 149946 Hom.: 14248 Cov.: 25 AF XY: 0.421 AC XY: 30809 AN XY: 73166

African (AFR) AF: 0.582 AC: 23602 AN: 40530

American (AMR) AF: 0.304 AC: 4516 AN: 14870

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3464

East Asian (EAS) AF: 0.472 AC: 2425 AN: 5134

South Asian (SAS) AF: 0.362 AC: 1712 AN: 4730

European-Finnish (FIN) AF: 0.421 AC: 4331 AN: 10282

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24111 AN: 67662

Other (OTH) AF: 0.413 AC: 858 AN: 2078

Alfa AF: 0.365 Hom.: 5577

Bravo AF: 0.419

Asia WGS AF: 0.467 AC: 1619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.52
PhyloP100		-2.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7782269; hg19: chr7-38318590;