chr12-130868535-G-A

Variant names:

• chr12-130868535-G-A
• rs10848236

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 0.229 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.222 AC: 9211 AN: 41518

American (AMR) AF: 0.243 AC: 3706 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3466

East Asian (EAS) AF: 0.186 AC: 962 AN: 5182

South Asian (SAS) AF: 0.146 AC: 707 AN: 4826

European-Finnish (FIN) AF: 0.298 AC: 3153 AN: 10578

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15645 AN: 67996

Other (OTH) AF: 0.236 AC: 499 AN: 2112

Alfa AF: 0.230 Hom.: 8114

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
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs10848236; hg19: chr12-131353080;