rs17658685

Variant names:

• chr12-91132971-C-T
• rs17658685

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 0.0386 in 152,208 control chromosomes in the GnomAD database, including 148 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 (148 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0573 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: 0.0386 AC: 5869 AN: 152090 Hom.: 147 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0479

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0588

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0386 AC: 5868 AN: 152208 Hom.: 148 Cov.: 32 AF XY: 0.0375 AC XY: 2790 AN XY: 74410

Gnomad4 AFR AF: 0.0104

Gnomad4 AMR AF: 0.0478

Gnomad4 ASJ AF: 0.0738

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.0240

Gnomad4 NFE AF: 0.0588

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.0516 Hom.: 41

Bravo AF: 0.0389

Asia WGS AF: 0.00722 AC: 25 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17658685; hg19: chr12-91526748;