rs4077725

chr4-55290975-G-A

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 0.276 in 151,978 control chromosomes in the GnomAD database, including 8,774 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 0.28 (8774 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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: 0.276 AC: 41915 AN: 151860 Hom.: 8739 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.276 AC: 41999 AN: 151978 Hom.: 8774 Cov.: 32 AF XY: 0.273 AC XY: 20292 AN XY: 74304

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.251

Alfa AF: 0.159 Hom.: 4862

Bravo AF: 0.297

Asia WGS AF: 0.227 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.1
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4077725; hg19: chr4-56157142;