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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRG		n.38278989A>G		intragenic_variant

Ensembl

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

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 v4.3

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;