4-130869346-C-T

Position:

• chr4-130869346-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;