rs12477038

Positions:

• chr2-200828053-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;