12-46962344-A-G

Variant names:

• chr12-46962344-A-G
• rs2250595

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 0.608 in 152,026 control chromosomes in the GnomAD database, including 30,325 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 0.61 (30325 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 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: 0.607 AC: 92253 AN: 151908 Hom.: 30258 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.608 AC: 92387 AN: 152026 Hom.: 30325 Cov.: 31 AF XY: 0.606 AC XY: 45032 AN XY: 74318

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.606

Alfa AF: 0.512 Hom.: 11292

Bravo AF: 0.644

Asia WGS AF: 0.707 AC: 2456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2250595; hg19: chr12-47356127;