4-117039490-G-A

Variant names:

• chr4-117039490-G-A
• rs298923

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 0.63 in 151,864 control chromosomes in the GnomAD database, including 30,733 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 0.63 (30733 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.779 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: 0.630 AC: 95536 AN: 151744 Hom.: 30703 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.630 AC: 95609 AN: 151864 Hom.: 30733 Cov.: 31 AF XY: 0.634 AC XY: 47077 AN XY: 74226

African (AFR) AF: 0.512 AC: 21188 AN: 41410

American (AMR) AF: 0.674 AC: 10239 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2318 AN: 3472

East Asian (EAS) AF: 0.789 AC: 4050 AN: 5134

South Asian (SAS) AF: 0.800 AC: 3864 AN: 4828

European-Finnish (FIN) AF: 0.714 AC: 7561 AN: 10584

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44366 AN: 67924

Other (OTH) AF: 0.573 AC: 1212 AN: 2114

Alfa AF: 0.526 Hom.: 1723

Bravo AF: 0.620

Asia WGS AF: 0.767 AC: 2665 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	1.1
DANN	Benign	0.46
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs298923; hg19: chr4-117960646;