rs4289500

Variant names:

• chr4-55772372-G-C
• rs4289500

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 0.261 in 152,050 control chromosomes in the GnomAD database, including 6,300 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 0.26 (6300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.681
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 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: 0.261 AC: 39685 AN: 151932 Hom.: 6282 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.261 AC: 39740 AN: 152050 Hom.: 6300 Cov.: 32 AF XY: 0.262 AC XY: 19498 AN XY: 74342

African (AFR) AF: 0.439 AC: 18194 AN: 41430

American (AMR) AF: 0.292 AC: 4470 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1219 AN: 5170

South Asian (SAS) AF: 0.175 AC: 843 AN: 4818

European-Finnish (FIN) AF: 0.184 AC: 1943 AN: 10588

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

European-Non Finnish (NFE) AF: 0.174 AC: 11857 AN: 67970

Other (OTH) AF: 0.242 AC: 510 AN: 2108

Alfa AF: 0.220 Hom.: 648

Bravo AF: 0.276

Asia WGS AF: 0.245 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.62
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs4289500; hg19: chr4-56638538;