rs11536857

Variant names:

• chr9-117701858-C-T
• rs11536857

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 0.0473 in 152,192 control chromosomes in the GnomAD database, including 237 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 0.047 (237 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0654 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: 0.0473 AC: 7200 AN: 152074 Hom.: 238 Cov.: 33

Gnomad AFR AF: 0.0127

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.0384

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.0456

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

GnomAD4 genome AF: 0.0473 AC: 7195 AN: 152192 Hom.: 237 Cov.: 33 AF XY: 0.0483 AC XY: 3593 AN XY: 74404

African (AFR) AF: 0.0126 AC: 524 AN: 41538

American (AMR) AF: 0.0434 AC: 664 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0384 AC: 133 AN: 3468

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5166

South Asian (SAS) AF: 0.0271 AC: 131 AN: 4826

European-Finnish (FIN) AF: 0.0992 AC: 1050 AN: 10590

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0670 AC: 4557 AN: 68006

Other (OTH) AF: 0.0446 AC: 94 AN: 2106

Alfa AF: 0.0605 Hom.: 87

Bravo AF: 0.0407

Asia WGS AF: 0.0120 AC: 42 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	4.8
DANN	Benign	0.77
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs11536857; hg19: chr9-120464136;