4-55802265-A-G

Variant names:

• chr4-55802265-A-G
• rs753129

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 0.235 in 152,216 control chromosomes in the GnomAD database, including 4,568 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 0.24 (4568 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

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 (EAS) allele frequency at 95% confidence interval = 0.489 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: 0.235 AC: 35772 AN: 152100 Hom.: 4567 Cov.: 33

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.235 AC: 35787 AN: 152216 Hom.: 4568 Cov.: 33 AF XY: 0.233 AC XY: 17374 AN XY: 74442

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.247

Alfa AF: 0.253 Hom.: 10436

Bravo AF: 0.239

Asia WGS AF: 0.348 AC: 1210 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	3.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs753129; hg19: chr4-56668431;