rs12936587

Positions:

• chr17-17640408-G-A

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 0.376 in 152,006 control chromosomes in the GnomAD database, including 11,331 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 0.38 (11331 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.978

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57057 AN: 151888 Hom.: 11334 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.376 AC: 57085 AN: 152006 Hom.: 11331 Cov.: 33 AF XY: 0.366 AC XY: 27209 AN XY: 74276

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.364

Alfa AF: 0.435 Hom.: 18254

Bravo AF: 0.378

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12936587; hg19: chr17-17543722;