rs180096

Positions:

• chr17-69946593-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 0.755 in 151,840 control chromosomes in the GnomAD database, including 44,267 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 0.75 (44267 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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: 0.755 AC: 114488 AN: 151722 Hom.: 44207 Cov.: 29

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.755 AC: 114607 AN: 151840 Hom.: 44267 Cov.: 29 AF XY: 0.758 AC XY: 56240 AN XY: 74174

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.739

Alfa AF: 0.671 Hom.: 25686

Bravo AF: 0.770

Asia WGS AF: 0.882 AC: 3067 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	0.47
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180096; hg19: chr17-67942734;