chr1-45325482-G-A

Variant names:

• chr1-45325482-G-A
• rs10890324

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 0.619 in 151,978 control chromosomes in the GnomAD database, including 32,076 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 0.62 (32076 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94014 AN: 151860 Hom.: 32074 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.619 AC: 94022 AN: 151978 Hom.: 32076 Cov.: 32 AF XY: 0.626 AC XY: 46504 AN XY: 74300

African (AFR) AF: 0.310 AC: 12842 AN: 41406

American (AMR) AF: 0.750 AC: 11443 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2410 AN: 3472

East Asian (EAS) AF: 0.813 AC: 4207 AN: 5174

South Asian (SAS) AF: 0.736 AC: 3545 AN: 4816

European-Finnish (FIN) AF: 0.757 AC: 7994 AN: 10564

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49228 AN: 67972

Other (OTH) AF: 0.671 AC: 1413 AN: 2106

Alfa AF: 0.699 Hom.: 64927

Bravo AF: 0.604

Asia WGS AF: 0.762 AC: 2646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.74
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10890324; hg19: chr1-45791154;