rs12601458

Variant names:

• chr17-27723510-C-A
• rs12601458

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 0.105 in 152,082 control chromosomes in the GnomAD database, including 1,141 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 (1141 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 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: 0.105 AC: 15882 AN: 151964 Hom.: 1127 Cov.: 31

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0788

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.105 AC: 15907 AN: 152082 Hom.: 1141 Cov.: 31 AF XY: 0.109 AC XY: 8094 AN XY: 74316

Gnomad4 AFR AF: 0.0274

Gnomad4 AMR AF: 0.0787

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.124

Alfa AF: 0.129 Hom.: 1636

Bravo AF: 0.0921

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12601458; hg19: chr17-26050536;