4-131103329-G-A

Variant names:

• chr4-131103329-G-A
• rs4864029

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 0.854 in 151,802 control chromosomes in the GnomAD database, including 55,850 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 0.85 (55850 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.907 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: 0.855 AC: 129646 AN: 151694 Hom.: 55839 Cov.: 30

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.854 AC: 129701 AN: 151802 Hom.: 55850 Cov.: 30 AF XY: 0.852 AC XY: 63182 AN XY: 74146

African (AFR) AF: 0.741 AC: 30629 AN: 41326

American (AMR) AF: 0.920 AC: 14054 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.936 AC: 3249 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4463 AN: 5150

South Asian (SAS) AF: 0.873 AC: 4201 AN: 4814

European-Finnish (FIN) AF: 0.815 AC: 8514 AN: 10442

Middle Eastern (MID) AF: 0.932 AC: 272 AN: 292

European-Non Finnish (NFE) AF: 0.906 AC: 61636 AN: 68002

Other (OTH) AF: 0.878 AC: 1853 AN: 2110

Alfa AF: 0.897 Hom.: 103661

Bravo AF: 0.857

Asia WGS AF: 0.876 AC: 3047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.15
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs4864029; hg19: chr4-132024484;