rs11105987

chr12-91100420-A-C

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 0.206 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.201

Alfa AF: 0.202 Hom.: 529

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11105987; hg19: chr12-91494197;