chr12-58865846-A-G

Variant names:

• chr12-58865846-A-G
• rs11172782

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 0.115 in 151,364 control chromosomes in the GnomAD database, including 2,238 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 0.11 (2238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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: 0.115 AC: 17363 AN: 151250 Hom.: 2234 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0266

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0736

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0152

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.115 AC: 17394 AN: 151364 Hom.: 2238 Cov.: 32 AF XY: 0.113 AC XY: 8356 AN XY: 74010

African (AFR) AF: 0.315 AC: 12963 AN: 41176

American (AMR) AF: 0.118 AC: 1784 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.0266 AC: 92 AN: 3464

East Asian (EAS) AF: 0.127 AC: 654 AN: 5132

South Asian (SAS) AF: 0.0732 AC: 351 AN: 4792

European-Finnish (FIN) AF: 0.0271 AC: 285 AN: 10520

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0152 AC: 1034 AN: 67818

Other (OTH) AF: 0.0958 AC: 201 AN: 2098

Alfa AF: 0.0470 Hom.: 2094

Bravo AF: 0.130

Asia WGS AF: 0.129 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs11172782; hg19: chr12-59259628;