chr12-113541851-C-G

Variant names:

• chr12-113541851-C-G
• rs11066587

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 0.135 in 152,170 control chromosomes in the GnomAD database, including 2,132 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 0.14 (2132 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.278 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: 0.135 AC: 20572 AN: 152052 Hom.: 2116 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0475

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0552

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.135 AC: 20616 AN: 152170 Hom.: 2132 Cov.: 33 AF XY: 0.139 AC XY: 10317 AN XY: 74394

African (AFR) AF: 0.282 AC: 11696 AN: 41472

American (AMR) AF: 0.100 AC: 1530 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0475 AC: 165 AN: 3472

East Asian (EAS) AF: 0.209 AC: 1079 AN: 5164

South Asian (SAS) AF: 0.0997 AC: 482 AN: 4834

European-Finnish (FIN) AF: 0.149 AC: 1581 AN: 10590

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0552 AC: 3758 AN: 68030

Other (OTH) AF: 0.108 AC: 228 AN: 2110

Alfa AF: 0.0735 Hom.: 374

Bravo AF: 0.137

Asia WGS AF: 0.153 AC: 533 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	2.8
DANN	Benign	0.61
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs11066587; hg19: chr12-113979656;