rs11636552

Variant names:

• chr15-25889808-T-G
• rs11636552

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 0.164 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
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.205 AC: 8519 AN: 41496

American (AMR) AF: 0.133 AC: 2039 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3472

East Asian (EAS) AF: 0.171 AC: 881 AN: 5158

South Asian (SAS) AF: 0.176 AC: 847 AN: 4822

European-Finnish (FIN) AF: 0.145 AC: 1532 AN: 10602

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10160 AN: 68004

Other (OTH) AF: 0.164 AC: 346 AN: 2116

Alfa AF: 0.156 Hom.: 1472

Bravo AF: 0.165

Asia WGS AF: 0.155 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.55
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs11636552; hg19: chr15-26134955;