17-17640408-G-A

Variant names:

• chr17-17640408-G-A
• rs12936587

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 0.376 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
• Publications: 117 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.376 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

African (AFR) AF: 0.297 AC: 12314 AN: 41478

American (AMR) AF: 0.382 AC: 5832 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1502 AN: 3472

East Asian (EAS) AF: 0.124 AC: 641 AN: 5170

South Asian (SAS) AF: 0.210 AC: 1011 AN: 4804

European-Finnish (FIN) AF: 0.331 AC: 3492 AN: 10548

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31031 AN: 67960

Other (OTH) AF: 0.364 AC: 770 AN: 2114

Alfa AF: 0.426 Hom.: 44638

Bravo AF: 0.378

Asia WGS AF: 0.192 AC: 668 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	0.20
DANN	Benign	0.32
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs12936587; hg19: chr17-17543722;