rs10877839

Variant names:

• chr12-62424701-T-C
• rs10877839

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 0.266 in 152,058 control chromosomes in the GnomAD database, including 6,638 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 0.27 (6638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.933

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 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: 0.266 AC: 40456 AN: 151942 Hom.: 6631 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.266 AC: 40463 AN: 152058 Hom.: 6638 Cov.: 32 AF XY: 0.274 AC XY: 20395 AN XY: 74332

Gnomad4 AFR AF: 0.0874

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.247

Alfa AF: 0.305 Hom.: 15332

Bravo AF: 0.249

Asia WGS AF: 0.300 AC: 1046 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10877839; hg19: chr12-62818481;