rs2046292

chr12-55847314-T-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 0.755 in 151,980 control chromosomes in the GnomAD database, including 48,073 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 0.75 (48073 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.933 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: 0.756 AC: 114732 AN: 151862 Hom.: 48082 Cov.: 30

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.939

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.755 AC: 114733 AN: 151980 Hom.: 48073 Cov.: 30 AF XY: 0.756 AC XY: 56173 AN XY: 74304

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.939

Gnomad4 OTH AF: 0.806

Alfa AF: 0.804 Hom.: 4903

Bravo AF: 0.733

Asia WGS AF: 0.781 AC: 2713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.2
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046292; hg19: chr12-56241098;