rs4845624

Variant names:

• chr1-151855337-G-A
• rs4845624

Your query was ambiguous. Multiple possible variants found:

• chr1-151855337-G-A
• chr1-151855337-G-C

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 0.529 in 152,048 control chromosomes in the GnomAD database, including 25,628 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 0.53 (25628 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 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: 0.529 AC: 80390 AN: 151932 Hom.: 25627 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.529 AC: 80403 AN: 152048 Hom.: 25628 Cov.: 32 AF XY: 0.534 AC XY: 39668 AN XY: 74354

African (AFR) AF: 0.167 AC: 6912 AN: 41432

American (AMR) AF: 0.609 AC: 9311 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1547 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3173 AN: 5172

South Asian (SAS) AF: 0.403 AC: 1942 AN: 4814

European-Finnish (FIN) AF: 0.819 AC: 8665 AN: 10580

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.692 AC: 47071 AN: 67980

Other (OTH) AF: 0.541 AC: 1143 AN: 2114

Alfa AF: 0.621 Hom.: 51075

Bravo AF: 0.500

Asia WGS AF: 0.479 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.69
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs4845624; hg19: chr1-151827813;