rs7017417

Variant names:

• chr8-27487788-A-G
• rs7017417

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 0.122 in 152,200 control chromosomes in the GnomAD database, including 1,180 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 0.12 (1180 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18536 AN: 152082 Hom.: 1175 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.0933

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.0886

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.122 AC: 18563 AN: 152200 Hom.: 1180 Cov.: 33 AF XY: 0.119 AC XY: 8824 AN XY: 74408

African (AFR) AF: 0.174 AC: 7233 AN: 41516

American (AMR) AF: 0.0932 AC: 1425 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0948 AC: 329 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5186

South Asian (SAS) AF: 0.0665 AC: 321 AN: 4826

European-Finnish (FIN) AF: 0.0886 AC: 940 AN: 10604

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7946 AN: 67998

Other (OTH) AF: 0.123 AC: 259 AN: 2108

Alfa AF: 0.115 Hom.: 1823

Bravo AF: 0.125

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.62
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7017417; hg19: chr8-27345305;