12-10614199-A-G

Variant names:

• chr12-10614199-A-G
• rs2219383

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 0.719 in 152,020 control chromosomes in the GnomAD database, including 40,997 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 0.72 (40997 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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: 0.719 AC: 109240 AN: 151902 Hom.: 40966 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.719 AC: 109320 AN: 152020 Hom.: 40997 Cov.: 31 AF XY: 0.723 AC XY: 53745 AN XY: 74318

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.742

Alfa AF: 0.783 Hom.: 61595

Bravo AF: 0.710

Asia WGS AF: 0.888 AC: 3089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2219383; hg19: chr12-10766798;