rs12358475

Positions:

• chr10-11806793-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;