rs11104775

Variant names:

• chr12-88245913-C-T
• rs11104775

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 0.0228 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
• Publications: 6 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 (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

African (AFR) AF: 0.00405 AC: 168 AN: 41524

American (AMR) AF: 0.0843 AC: 1288 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3470

East Asian (EAS) AF: 0.138 AC: 712 AN: 5176

South Asian (SAS) AF: 0.0135 AC: 65 AN: 4808

European-Finnish (FIN) AF: 0.0233 AC: 247 AN: 10584

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0130 AC: 883 AN: 67988

Other (OTH) AF: 0.0232 AC: 49 AN: 2116

Alfa AF: 0.0165 Hom.: 72

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs11104775; hg19: chr12-88639690;