1-151836388-C-G

Variant names:

• chr1-151836388-C-G
• rs4845366

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 0.787 in 152,016 control chromosomes in the GnomAD database, including 47,497 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 0.79 (47497 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 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: 0.787 AC: 119536 AN: 151898 Hom.: 47467 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.787 AC: 119619 AN: 152016 Hom.: 47497 Cov.: 31 AF XY: 0.789 AC XY: 58604 AN XY: 74312

African (AFR) AF: 0.677 AC: 28048 AN: 41414

American (AMR) AF: 0.823 AC: 12565 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3148 AN: 3468

East Asian (EAS) AF: 0.833 AC: 4303 AN: 5168

South Asian (SAS) AF: 0.810 AC: 3893 AN: 4806

European-Finnish (FIN) AF: 0.833 AC: 8817 AN: 10580

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56158 AN: 67998

Other (OTH) AF: 0.807 AC: 1706 AN: 2114

Alfa AF: 0.804 Hom.: 5803

Bravo AF: 0.781

Asia WGS AF: 0.803 AC: 2789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.44
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4845366; hg19: chr1-151808864;