rs12410462

Variant names:

• chr1-227480089-G-A
• rs12410462

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 0.124 in 152,228 control chromosomes in the GnomAD database, including 1,223 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 0.12 (1223 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.163 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: 0.123 AC: 18785 AN: 152110 Hom.: 1220 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0942

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.124 AC: 18809 AN: 152228 Hom.: 1223 Cov.: 32 AF XY: 0.122 AC XY: 9047 AN XY: 74426

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0942

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.119

Alfa AF: 0.124 Hom.: 199

Bravo AF: 0.125

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.19
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12410462; hg19: chr1-227667790; COSMIC: COSV69473744;