rs11636552

Variant names:

• chr15-25889808-T-G
• rs11636552

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 0.164 in 152,178 control chromosomes in the GnomAD database, including 2,027 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 0.16 (2027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315

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 = 0.202 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: 0.164 AC: 24899 AN: 152060 Hom.: 2025 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.164 AC: 24924 AN: 152178 Hom.: 2027 Cov.: 32 AF XY: 0.163 AC XY: 12098 AN XY: 74402

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.164

Alfa AF: 0.155 Hom.: 1056

Bravo AF: 0.165

Asia WGS AF: 0.155 AC: 541 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	3.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11636552; hg19: chr15-26134955;