chr12-55847314-T-G

Variant names:

• chr12-55847314-T-G
• rs2046292

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 0.755 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.357 AC: 14755 AN: 41384

American (AMR) AF: 0.819 AC: 12490 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3127 AN: 3470

East Asian (EAS) AF: 0.752 AC: 3875 AN: 5152

South Asian (SAS) AF: 0.823 AC: 3960 AN: 4810

European-Finnish (FIN) AF: 0.931 AC: 9857 AN: 10584

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.939 AC: 63841 AN: 68014

Other (OTH) AF: 0.806 AC: 1699 AN: 2108

Alfa AF: 0.811 Hom.: 9567

Bravo AF: 0.733

Asia WGS AF: 0.781 AC: 2713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.43
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2046292; hg19: chr12-56241098;