rs10848236

chr12-130868535-G-A

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 0.229 in 152,152 control chromosomes in the GnomAD database, including 4,022 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 0.23 (4022 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927

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 (AMR) allele frequency at 95% confidence interval = 0.236 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: 0.230 AC: 34895 AN: 152034 Hom.: 4020 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.229 AC: 34918 AN: 152152 Hom.: 4022 Cov.: 33 AF XY: 0.231 AC XY: 17215 AN XY: 74390

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.236

Alfa AF: 0.230 Hom.: 4991

Bravo AF: 0.228

Asia WGS AF: 0.167 AC: 583 AN: 3478

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	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10848236; hg19: chr12-131353080;