rs11104870

Variant names:

• chr12-88435517-C-T
• rs11104870

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 0.566 in 152,046 control chromosomes in the GnomAD database, including 28,173 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 0.57 (28173 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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: 0.566 AC: 86026 AN: 151928 Hom.: 28171 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.566 AC: 86029 AN: 152046 Hom.: 28173 Cov.: 32 AF XY: 0.568 AC XY: 42221 AN XY: 74320

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.627

Alfa AF: 0.605 Hom.: 3949

Bravo AF: 0.560

Asia WGS AF: 0.680 AC: 2363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.22
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11104870; hg19: chr12-88829294;