rs11536857

Variant names:

• chr9-117701858-C-T
• rs11536857

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 0.0473 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

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 (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

Gnomad4 AFR AF: 0.0126

Gnomad4 AMR AF: 0.0434

Gnomad4 ASJ AF: 0.0384

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0271

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.0446

Alfa AF: 0.0544 Hom.: 29

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11536857; hg19: chr9-120464136;