rs10877839

Positions:

• chr12-62424701-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;