rs17058916

Positions:

• chr18-76110782-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 0.0393 in 152,122 control chromosomes in the GnomAD database, including 288 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 0.039 (288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 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: 0.0394 AC: 5983 AN: 152004 Hom.: 287 Cov.: 32

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0721

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0778

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0393 AC: 5983 AN: 152122 Hom.: 288 Cov.: 32 AF XY: 0.0445 AC XY: 3310 AN XY: 74356

Gnomad4 AFR AF: 0.0180

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0721

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.0777

Gnomad4 FIN AF: 0.0505

Gnomad4 NFE AF: 0.0177

Gnomad4 OTH AF: 0.0436

Alfa AF: 0.0264 Hom.: 19

Bravo AF: 0.0442

Asia WGS AF: 0.129 AC: 446 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	0.0040
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17058916; hg19: chr18-73822737;