rs10877107

Variant names:

• chr12-58359477-C-A
• rs10877107

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 0.0527 in 152,262 control chromosomes in the GnomAD database, including 341 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 0.053 (341 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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: 0.0527 AC: 8014 AN: 152144 Hom.: 340 Cov.: 33

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0525

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

GnomAD4 genome AF: 0.0527 AC: 8020 AN: 152262 Hom.: 341 Cov.: 33 AF XY: 0.0531 AC XY: 3952 AN XY: 74440

Gnomad4 AFR AF: 0.0525

Gnomad4 AMR AF: 0.0798

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.0821

Gnomad4 FIN AF: 0.0227

Gnomad4 NFE AF: 0.0384

Gnomad4 OTH AF: 0.0510

Alfa AF: 0.0558 Hom.: 41

Bravo AF: 0.0593

Asia WGS AF: 0.123 AC: 427 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10877107; hg19: chr12-58753260;