10-32390904-C-G

Variant names:

• chr10-32390904-C-G
• rs7079770

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 0.363 in 150,796 control chromosomes in the GnomAD database, including 10,469 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 0.36 (10469 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 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: 0.362 AC: 54620 AN: 150706 Hom.: 10443 Cov.: 29

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.363 AC: 54683 AN: 150796 Hom.: 10469 Cov.: 29 AF XY: 0.365 AC XY: 26809 AN XY: 73528

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.344

Alfa AF: 0.328 Hom.: 1016

Bravo AF: 0.369

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7079770; hg19: chr10-32679832;