rs12358475

Variant names:

• chr10-11806793-G-A
• rs12358475

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 0.168 in 152,162 control chromosomes in the GnomAD database, including 2,811 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 0.17 (2811 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.238 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: 0.168 AC: 25572 AN: 152044 Hom.: 2809 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.168 AC: 25575 AN: 152162 Hom.: 2811 Cov.: 32 AF XY: 0.168 AC XY: 12484 AN XY: 74400

Gnomad4 AFR AF: 0.0436

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.00443

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.160

Alfa AF: 0.219 Hom.: 8003

Bravo AF: 0.153

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12358475; hg19: chr10-11848792;