rs11104870

Variant names:

• chr12-88435517-C-T
• rs11104870

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 0.566 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
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.215 AC: 8924 AN: 41464

American (AMR) AF: 0.709 AC: 10837 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2723 AN: 3468

East Asian (EAS) AF: 0.777 AC: 4013 AN: 5168

South Asian (SAS) AF: 0.690 AC: 3330 AN: 4826

European-Finnish (FIN) AF: 0.565 AC: 5962 AN: 10560

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48082 AN: 67960

Other (OTH) AF: 0.627 AC: 1322 AN: 2110

Alfa AF: 0.643 Hom.: 54368

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11104870; hg19: chr12-88829294;