1-46414184-C-G

Position:

• chr1-46414184-C-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 0.695 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.820

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.714

Alfa AF: 0.495 Hom.: 608

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12029329; hg19: chr1-46879856;