chr1-46224659-G-C

Variant names:

• chr1-46224659-G-C
• rs12028248

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 0.677 in 151,704 control chromosomes in the GnomAD database, including 35,913 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 0.68 (35913 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 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: 0.678 AC: 102735 AN: 151586 Hom.: 35922 Cov.: 29

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.677 AC: 102768 AN: 151704 Hom.: 35913 Cov.: 29 AF XY: 0.677 AC XY: 50165 AN XY: 74142

African (AFR) AF: 0.489 AC: 20208 AN: 41314

American (AMR) AF: 0.689 AC: 10496 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2769 AN: 3470

East Asian (EAS) AF: 0.850 AC: 4376 AN: 5148

South Asian (SAS) AF: 0.717 AC: 3428 AN: 4780

European-Finnish (FIN) AF: 0.681 AC: 7164 AN: 10520

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51835 AN: 67942

Other (OTH) AF: 0.723 AC: 1521 AN: 2104

Alfa AF: 0.695 Hom.: 4662

Bravo AF: 0.672

Asia WGS AF: 0.761 AC: 2643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs12028248; hg19: chr1-46690331;