15-90528542-T-C

Variant names:

• chr15-90528542-T-C
• rs11635252

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 0.875 in 152,136 control chromosomes in the GnomAD database, including 58,432 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 0.87 (58432 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133023 AN: 152018 Hom.: 58400 Cov.: 31

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.875 AC: 133106 AN: 152136 Hom.: 58432 Cov.: 31 AF XY: 0.872 AC XY: 64859 AN XY: 74368

African (AFR) AF: 0.858 AC: 35594 AN: 41508

American (AMR) AF: 0.807 AC: 12323 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 3250 AN: 3464

East Asian (EAS) AF: 0.767 AC: 3968 AN: 5176

South Asian (SAS) AF: 0.776 AC: 3747 AN: 4826

European-Finnish (FIN) AF: 0.910 AC: 9622 AN: 10578

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61587 AN: 67988

Other (OTH) AF: 0.888 AC: 1875 AN: 2112

Alfa AF: 0.881 Hom.: 17108

Bravo AF: 0.867

Asia WGS AF: 0.787 AC: 2736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.44
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs11635252; hg19: chr15-91071774;