rs10877107

Variant names:

• chr12-58359477-C-A
• rs10877107

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 0.0527 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0525 AC: 2180 AN: 41554

American (AMR) AF: 0.0798 AC: 1221 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1080 AN: 5178

South Asian (SAS) AF: 0.0821 AC: 395 AN: 4812

European-Finnish (FIN) AF: 0.0227 AC: 241 AN: 10610

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0384 AC: 2610 AN: 68010

Other (OTH) AF: 0.0510 AC: 108 AN: 2116

Alfa AF: 0.0557 Hom.: 42

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10877107; hg19: chr12-58753260;