rs17658598

Variant names:

• chr12-91129497-A-G
• rs17658598

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 0.0882 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0240 AC: 997 AN: 41518

American (AMR) AF: 0.0989 AC: 1506 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5180

South Asian (SAS) AF: 0.0421 AC: 203 AN: 4822

European-Finnish (FIN) AF: 0.0842 AC: 891 AN: 10584

Middle Eastern (MID) AF: 0.0764 AC: 22 AN: 288

European-Non Finnish (NFE) AF: 0.133 AC: 9040 AN: 67906

Other (OTH) AF: 0.105 AC: 222 AN: 2106

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs17658598; hg19: chr12-91523274;