rs1478089

Variant names:

• chr4-130853495-A-C
• rs1478089

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 0.0572 in 152,252 control chromosomes in the GnomAD database, including 681 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 0.057 (681 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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: 0.0571 AC: 8684 AN: 152134 Hom.: 677 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0479

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.00642

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00187

Gnomad OTH AF: 0.0463

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

GnomAD4 genome AF: 0.0572 AC: 8716 AN: 152252 Hom.: 681 Cov.: 32 AF XY: 0.0560 AC XY: 4166 AN XY: 74458

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0479

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.0288

Gnomad4 SAS AF: 0.00663

Gnomad4 FIN AF: 0.0277

Gnomad4 NFE AF: 0.00187

Gnomad4 OTH AF: 0.0458

Alfa AF: 0.0358 Hom.: 53

Bravo AF: 0.0648

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1478089; hg19: chr4-131774650;