rs17658598

chr12-91129497-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 0.0882 in 152,008 control chromosomes in the GnomAD database, including 778 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 0.088 (778 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 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: 0.0882 AC: 13398 AN: 151888 Hom.: 775 Cov.: 32

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0987

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.0812

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0882 AC: 13402 AN: 152008 Hom.: 778 Cov.: 32 AF XY: 0.0858 AC XY: 6376 AN XY: 74290

Gnomad4 AFR AF: 0.0240

Gnomad4 AMR AF: 0.0989

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0421

Gnomad4 FIN AF: 0.0842

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0954 Hom.: 122

Bravo AF: 0.0869

Asia WGS AF: 0.0230 AC: 78 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.070
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17658598; hg19: chr12-91523274;