15-45426989-G-C

Variant names:

• chr15-45426989-G-C
• rs17536527

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 0.461 in 152,046 control chromosomes in the GnomAD database, including 17,372 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 0.46 (17372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70063 AN: 151930 Hom.: 17358 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.461 AC: 70107 AN: 152046 Hom.: 17372 Cov.: 32 AF XY: 0.473 AC XY: 35153 AN XY: 74318

African (AFR) AF: 0.349 AC: 14470 AN: 41452

American (AMR) AF: 0.636 AC: 9721 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2033 AN: 3470

East Asian (EAS) AF: 0.919 AC: 4770 AN: 5190

South Asian (SAS) AF: 0.558 AC: 2688 AN: 4814

European-Finnish (FIN) AF: 0.477 AC: 5032 AN: 10550

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.440 AC: 29906 AN: 67978

Other (OTH) AF: 0.503 AC: 1062 AN: 2112

Alfa AF: 0.270 Hom.: 609

Bravo AF: 0.472

Asia WGS AF: 0.689 AC: 2391 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.32
DANN	Benign	0.76
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs17536527; hg19: chr15-45719187;