rs427488

Variant names:

• chr17-12524920-A-G
• rs427488

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 0.152 in 152,132 control chromosomes in the GnomAD database, including 3,294 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 0.15 (3294 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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: 0.152 AC: 23141 AN: 152012 Hom.: 3283 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0960

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0620

Gnomad FIN AF: 0.0432

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0584

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.152 AC: 23192 AN: 152132 Hom.: 3294 Cov.: 32 AF XY: 0.149 AC XY: 11107 AN XY: 74372

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.0962

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0620

Gnomad4 FIN AF: 0.0432

Gnomad4 NFE AF: 0.0584

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0742 Hom.: 975

Bravo AF: 0.169

Asia WGS AF: 0.115 AC: 401 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs427488; hg19: chr17-12428237;