4-117269425-G-A

Variant names:

• chr4-117269425-G-A
• rs12644393

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 0.432 in 151,672 control chromosomes in the GnomAD database, including 14,604 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 0.43 (14604 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.551 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: 0.432 AC: 65542 AN: 151554 Hom.: 14584 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.432 AC: 65592 AN: 151672 Hom.: 14604 Cov.: 32 AF XY: 0.438 AC XY: 32478 AN XY: 74106

African (AFR) AF: 0.347 AC: 14357 AN: 41410

American (AMR) AF: 0.561 AC: 8491 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1594 AN: 3466

East Asian (EAS) AF: 0.259 AC: 1328 AN: 5134

South Asian (SAS) AF: 0.456 AC: 2195 AN: 4814

European-Finnish (FIN) AF: 0.494 AC: 5208 AN: 10546

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 30988 AN: 67848

Other (OTH) AF: 0.477 AC: 1003 AN: 2104

Alfa AF: 0.459 Hom.: 24944

Bravo AF: 0.433

Asia WGS AF: 0.371 AC: 1291 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.56
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs12644393; hg19: chr4-118190581;