rs12406383

Variant names:

• chr1-11861936-C-A
• rs12406383

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 0.25 in 152,066 control chromosomes in the GnomAD database, including 4,868 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 0.25 (4868 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.315 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: 0.251 AC: 38072 AN: 151946 Hom.: 4871 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.250 AC: 38091 AN: 152066 Hom.: 4868 Cov.: 31 AF XY: 0.249 AC XY: 18519 AN XY: 74328

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.262

Alfa AF: 0.259 Hom.: 1003

Bravo AF: 0.243

Asia WGS AF: 0.265 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12406383; hg19: chr1-11921993; COSMIC: COSV64687436;