rs11104775

Variant names:

• chr12-88245913-C-T
• rs11104775

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 0.0228 in 152,146 control chromosomes in the GnomAD database, including 161 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 0.023 (161 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 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: 0.0228 AC: 3460 AN: 152028 Hom.: 158 Cov.: 32

Gnomad AFR AF: 0.00406

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.0233

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0228 AC: 3465 AN: 152146 Hom.: 161 Cov.: 32 AF XY: 0.0242 AC XY: 1803 AN XY: 74366

Gnomad4 AFR AF: 0.00405

Gnomad4 AMR AF: 0.0843

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0135

Gnomad4 FIN AF: 0.0233

Gnomad4 NFE AF: 0.0130

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0147 Hom.: 47

Bravo AF: 0.0265

Asia WGS AF: 0.0800 AC: 279 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11104775; hg19: chr12-88639690;