rs4077725

Variant names:

• chr4-55290975-G-A
• rs4077725

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 0.276 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.589 AC: 24372 AN: 41386

American (AMR) AF: 0.211 AC: 3219 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1401 AN: 5156

South Asian (SAS) AF: 0.151 AC: 725 AN: 4816

European-Finnish (FIN) AF: 0.156 AC: 1657 AN: 10590

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9379 AN: 67970

Other (OTH) AF: 0.251 AC: 530 AN: 2110

Alfa AF: 0.184 Hom.: 11796

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4077725; hg19: chr4-56157142;