rs12477038

Variant names:

• chr2-200828053-T-C
• rs12477038

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 0.101 in 152,236 control chromosomes in the GnomAD database, including 1,098 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 0.10 (1098 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 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: 0.101 AC: 15362 AN: 152118 Hom.: 1092 Cov.: 32

Gnomad AFR AF: 0.0286

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0986

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.101 AC: 15367 AN: 152236 Hom.: 1098 Cov.: 32 AF XY: 0.105 AC XY: 7825 AN XY: 74438

Gnomad4 AFR AF: 0.0286

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.0986

Gnomad4 OTH AF: 0.110

Alfa AF: 0.109 Hom.: 1422

Bravo AF: 0.104

Asia WGS AF: 0.205 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12477038; hg19: chr2-201692776;