rs17679451

Variant names:

• chr17-36106925-G-A
• rs17679451

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 0.0452 in 152,268 control chromosomes in the GnomAD database, including 203 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 0.045 (203 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.826
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0518 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: 0.0451 AC: 6868 AN: 152150 Hom.: 202 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0474

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0452 AC: 6879 AN: 152268 Hom.: 203 Cov.: 32 AF XY: 0.0430 AC XY: 3203 AN XY: 74472

African (AFR) AF: 0.0535 AC: 2221 AN: 41542

American (AMR) AF: 0.0342 AC: 523 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0657 AC: 228 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0574 AC: 277 AN: 4828

European-Finnish (FIN) AF: 0.0232 AC: 246 AN: 10610

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0474 AC: 3224 AN: 68018

Other (OTH) AF: 0.0473 AC: 100 AN: 2114

Alfa AF: 0.0484 Hom.: 64

Bravo AF: 0.0454

Asia WGS AF: 0.0240 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.63
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs17679451; hg19: chr17-34434318;