1-46420268-A-C

Variant names:

• chr1-46420268-A-C
• rs4660928

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 0.641 in 152,164 control chromosomes in the GnomAD database, including 32,413 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 0.64 (32413 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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: 0.641 AC: 97460 AN: 152046 Hom.: 32413 Cov.: 33

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.641 AC: 97512 AN: 152164 Hom.: 32413 Cov.: 33 AF XY: 0.641 AC XY: 47692 AN XY: 74384

African (AFR) AF: 0.456 AC: 18938 AN: 41504

American (AMR) AF: 0.647 AC: 9889 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2689 AN: 3472

East Asian (EAS) AF: 0.827 AC: 4285 AN: 5184

South Asian (SAS) AF: 0.733 AC: 3538 AN: 4824

European-Finnish (FIN) AF: 0.639 AC: 6761 AN: 10576

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 48992 AN: 67994

Other (OTH) AF: 0.684 AC: 1445 AN: 2114

Alfa AF: 0.702 Hom.: 162297

Bravo AF: 0.633

Asia WGS AF: 0.771 AC: 2679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.35
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs4660928; hg19: chr1-46885940;