chr1-152482115-G-A

Variant names:

• chr1-152482115-G-A
• rs908922

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 0.774 in 152,024 control chromosomes in the GnomAD database, including 45,774 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 0.77 (45774 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 16 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 (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117495 AN: 151908 Hom.: 45727 Cov.: 30

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.774 AC: 117597 AN: 152024 Hom.: 45774 Cov.: 30 AF XY: 0.776 AC XY: 57677 AN XY: 74304

African (AFR) AF: 0.883 AC: 36655 AN: 41494

American (AMR) AF: 0.771 AC: 11766 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2791 AN: 3470

East Asian (EAS) AF: 0.764 AC: 3944 AN: 5160

South Asian (SAS) AF: 0.718 AC: 3447 AN: 4800

European-Finnish (FIN) AF: 0.771 AC: 8143 AN: 10564

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48244 AN: 67956

Other (OTH) AF: 0.785 AC: 1660 AN: 2114

Alfa AF: 0.746 Hom.: 32662

Bravo AF: 0.780

Asia WGS AF: 0.765 AC: 2662 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	0.68
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs908922; hg19: chr1-152454591;