4-130869346-C-T

Variant names:

• chr4-130869346-C-T
• rs1478091

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 0.834 in 152,150 control chromosomes in the GnomAD database, including 54,446 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 0.83 (54446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.596
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126825 AN: 152034 Hom.: 54425 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.834 AC: 126890 AN: 152150 Hom.: 54446 Cov.: 32 AF XY: 0.836 AC XY: 62153 AN XY: 74380

African (AFR) AF: 0.605 AC: 25117 AN: 41490

American (AMR) AF: 0.881 AC: 13469 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3195 AN: 3470

East Asian (EAS) AF: 0.936 AC: 4838 AN: 5170

South Asian (SAS) AF: 0.882 AC: 4255 AN: 4822

European-Finnish (FIN) AF: 0.910 AC: 9636 AN: 10586

Middle Eastern (MID) AF: 0.887 AC: 259 AN: 292

European-Non Finnish (NFE) AF: 0.933 AC: 63481 AN: 68018

Other (OTH) AF: 0.847 AC: 1786 AN: 2108

Alfa AF: 0.903 Hom.: 260277

Bravo AF: 0.821

Asia WGS AF: 0.867 AC: 3011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.71
DANN	Benign	0.29
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs1478091; hg19: chr4-131790501;