rs17018627

chr12-91059593-A-Cchr12-91059593-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 0.102 in 151,114 control chromosomes in the GnomAD database, including 948 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 0.10 (948 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 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: 0.102 AC: 15341 AN: 150996 Hom.: 943 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0700

Gnomad SAS AF: 0.0409

Gnomad FIN AF: 0.0488

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0966

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

GnomAD4 genome AF: 0.102 AC: 15366 AN: 151114 Hom.: 948 Cov.: 32 AF XY: 0.0987 AC XY: 7290 AN XY: 73828

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0756

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0700

Gnomad4 SAS AF: 0.0409

Gnomad4 FIN AF: 0.0488

Gnomad4 NFE AF: 0.0782

Gnomad4 OTH AF: 0.0999

Alfa AF: 0.0604 Hom.: 141

Bravo AF: 0.108

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.69
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17018627; hg19: chr12-91453370;