rs11104868

Variant names:

• chr12-88434665-G-A
• rs11104868

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 0.269 in 152,114 control chromosomes in the GnomAD database, including 8,079 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 0.27 (8079 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 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: 0.269 AC: 40841 AN: 151996 Hom.: 8039 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.269 AC: 40933 AN: 152114 Hom.: 8079 Cov.: 33 AF XY: 0.270 AC XY: 20059 AN XY: 74378

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.234

Alfa AF: 0.153 Hom.: 4594

Bravo AF: 0.274

Asia WGS AF: 0.258 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
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: rs11104868; hg19: chr12-88828442;