rs12403821

Variant names:

• chr1-198323673-C-T
• rs12403821

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 0.17 in 152,030 control chromosomes in the GnomAD database, including 3,036 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 (3036 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 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: 0.170 AC: 25863 AN: 151912 Hom.: 3021 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.0968

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0917

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.170 AC: 25917 AN: 152030 Hom.: 3036 Cov.: 32 AF XY: 0.172 AC XY: 12765 AN XY: 74318

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.0967

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.0851

Gnomad4 NFE AF: 0.0917

Gnomad4 OTH AF: 0.177

Alfa AF: 0.123 Hom.: 694

Bravo AF: 0.186

Asia WGS AF: 0.201 AC: 700 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12403821; hg19: chr1-198292803;