4-130869346-C-T

Variant names:

• chr4-130869346-C-T
• rs1478091

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.933

Gnomad4 OTH AF: 0.847

Alfa AF: 0.918 Hom.: 139191

Bravo AF: 0.821

Asia WGS AF: 0.867 AC: 3011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1478091; hg19: chr4-131790501;