rs7017417

chr8-27487788-A-G

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 0.122 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0932

Gnomad4 ASJ AF: 0.0948

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0665

Gnomad4 FIN AF: 0.0886

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.123

Alfa AF: 0.112 Hom.: 1353

Bravo AF: 0.125

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.3
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7017417; hg19: chr8-27345305;