rs12257237

Variant names:

• chr10-6393195-G-C
• rs12257237

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 0.137 in 152,044 control chromosomes in the GnomAD database, including 1,525 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 0.14 (1525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 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: 0.137 AC: 20763 AN: 151924 Hom.: 1520 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.0933

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.137 AC: 20799 AN: 152044 Hom.: 1525 Cov.: 32 AF XY: 0.140 AC XY: 10404 AN XY: 74330

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0932

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.117

Alfa AF: 0.121 Hom.: 156

Bravo AF: 0.130

Asia WGS AF: 0.177 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12257237; hg19: chr10-6435157;