rs11105987

Variant names:

• chr12-91100420-A-C
• rs11105987

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 0.206 in 151,920 control chromosomes in the GnomAD database, including 3,799 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 0.21 (3799 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 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: 0.206 AC: 31278 AN: 151802 Hom.: 3779 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.206 AC: 31331 AN: 151920 Hom.: 3799 Cov.: 32 AF XY: 0.203 AC XY: 15093 AN XY: 74268

African (AFR) AF: 0.330 AC: 13652 AN: 41408

American (AMR) AF: 0.178 AC: 2715 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3468

East Asian (EAS) AF: 0.318 AC: 1636 AN: 5148

South Asian (SAS) AF: 0.147 AC: 710 AN: 4824

European-Finnish (FIN) AF: 0.107 AC: 1132 AN: 10606

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10187 AN: 67924

Other (OTH) AF: 0.201 AC: 424 AN: 2110

Alfa AF: 0.207 Hom.: 580

Bravo AF: 0.220

Asia WGS AF: 0.250 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.77
DANN	Benign	0.61
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs11105987; hg19: chr12-91494197;