rs10877945

Positions:

• chr12-63052182-G-A
• chr12-63052182-G-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 0.363 in 151,946 control chromosomes in the GnomAD database, including 10,663 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 (10663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 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: 0.363 AC: 55138 AN: 151828 Hom.: 10662 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.363 AC: 55153 AN: 151946 Hom.: 10663 Cov.: 32 AF XY: 0.362 AC XY: 26862 AN XY: 74260

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.369

Alfa AF: 0.405 Hom.: 12979

Bravo AF: 0.348

Asia WGS AF: 0.369 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10877945; hg19: chr12-63445962;