1-46414184-C-G

Variant names:

• chr1-46414184-C-G
• rs12029329

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 0.695 in 152,140 control chromosomes in the GnomAD database, including 37,253 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 0.70 (37253 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.696 AC: 105763 AN: 152022 Hom.: 37251 Cov.: 33

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.695 AC: 105806 AN: 152140 Hom.: 37253 Cov.: 33 AF XY: 0.696 AC XY: 51787 AN XY: 74370

African (AFR) AF: 0.586 AC: 24327 AN: 41486

American (AMR) AF: 0.675 AC: 10303 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2844 AN: 3470

East Asian (EAS) AF: 0.823 AC: 4262 AN: 5180

South Asian (SAS) AF: 0.756 AC: 3647 AN: 4822

European-Finnish (FIN) AF: 0.708 AC: 7499 AN: 10590

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50422 AN: 68008

Other (OTH) AF: 0.714 AC: 1505 AN: 2108

Alfa AF: 0.597 Hom.: 1682

Bravo AF: 0.687

Asia WGS AF: 0.767 AC: 2665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.88
DANN	Benign	0.45
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs12029329; hg19: chr1-46879856;