7-38254513-G-C

Variant names:

• chr7-38254513-G-C
• rs6462825

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 0.251 in 151,316 control chromosomes in the GnomAD database, including 4,972 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 0.25 (4972 hom., cov: 28)
• Consequence: TRG intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 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: 0.251 AC: 37931 AN: 151198 Hom.: 4964 Cov.: 28

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.251 AC: 37963 AN: 151316 Hom.: 4972 Cov.: 28 AF XY: 0.252 AC XY: 18624 AN XY: 73888

African (AFR) AF: 0.267 AC: 11002 AN: 41142

American (AMR) AF: 0.192 AC: 2920 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 908 AN: 3460

East Asian (EAS) AF: 0.322 AC: 1657 AN: 5146

South Asian (SAS) AF: 0.298 AC: 1422 AN: 4774

European-Finnish (FIN) AF: 0.271 AC: 2825 AN: 10436

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16524 AN: 67870

Other (OTH) AF: 0.241 AC: 506 AN: 2098

Alfa AF: 0.148 Hom.: 317

Bravo AF: 0.244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.46
PhyloP100		-1.1

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: rs6462825; hg19: chr7-38294114;