12-83614496-A-G

Variant names:

• chr12-83614496-A-G
• rs2403106

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.161 AC: 6687 AN: 41488

American (AMR) AF: 0.0602 AC: 920 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 287 AN: 3468

East Asian (EAS) AF: 0.120 AC: 618 AN: 5148

South Asian (SAS) AF: 0.109 AC: 526 AN: 4828

European-Finnish (FIN) AF: 0.217 AC: 2293 AN: 10580

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0787 AC: 5353 AN: 68004

Other (OTH) AF: 0.0967 AC: 204 AN: 2110

Alfa AF: 0.0876 Hom.: 2270

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
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs2403106; hg19: chr12-84008275;