rs2403106

chr12-83614496-A-G

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 0.112 in 152,106 control chromosomes in the GnomAD database, including 1,143 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 0.11 (1143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16982 AN: 151988 Hom.: 1138 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0787

Gnomad OTH AF: 0.0958

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

GnomAD4 genome AF: 0.112 AC: 17006 AN: 152106 Hom.: 1143 Cov.: 32 AF XY: 0.116 AC XY: 8619 AN XY: 74312

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0602

Gnomad4 ASJ AF: 0.0828

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.0787

Gnomad4 OTH AF: 0.0967

Alfa AF: 0.0849 Hom.: 904

Bravo AF: 0.100

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.15
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2403106; hg19: chr12-84008275;