10-117558293-C-G

Variant names:

• chr10-117558293-C-G
• rs4752078

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.491 in 152,080 control chromosomes in the GnomAD database, including 20,291 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 0.49 (20291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74601 AN: 151962 Hom.: 20285 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.491 AC: 74637 AN: 152080 Hom.: 20291 Cov.: 32 AF XY: 0.487 AC XY: 36205 AN XY: 74316

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.555

Alfa AF: 0.536 Hom.: 2823

Bravo AF: 0.492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4752078; hg19: chr10-119317804;