7-117252792-T-C

Variant names:

• chr7-117252792-T-C
• rs38904

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 0.511 in 151,980 control chromosomes in the GnomAD database, including 20,753 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 0.51 (20753 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 35 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77611 AN: 151862 Hom.: 20717 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.511 AC: 77703 AN: 151980 Hom.: 20753 Cov.: 32 AF XY: 0.503 AC XY: 37378 AN XY: 74260

African (AFR) AF: 0.675 AC: 27971 AN: 41420

American (AMR) AF: 0.463 AC: 7077 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1473 AN: 3464

East Asian (EAS) AF: 0.310 AC: 1602 AN: 5172

South Asian (SAS) AF: 0.422 AC: 2030 AN: 4814

European-Finnish (FIN) AF: 0.389 AC: 4108 AN: 10548

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31899 AN: 67964

Other (OTH) AF: 0.491 AC: 1036 AN: 2112

Alfa AF: 0.484 Hom.: 58115

Bravo AF: 0.525

Asia WGS AF: 0.392 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.8
DANN	Benign	0.14
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs38904; hg19: chr7-116892846;