4-55802265-A-G

Variant names:

• chr4-55802265-A-G
• rs753129

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 0.235 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
• Publications: 15 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 (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

African (AFR) AF: 0.179 AC: 7415 AN: 41528

American (AMR) AF: 0.255 AC: 3894 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1320 AN: 3470

East Asian (EAS) AF: 0.505 AC: 2618 AN: 5180

South Asian (SAS) AF: 0.318 AC: 1534 AN: 4818

European-Finnish (FIN) AF: 0.180 AC: 1915 AN: 10614

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16331 AN: 67992

Other (OTH) AF: 0.247 AC: 521 AN: 2112

Alfa AF: 0.250 Hom.: 20643

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs753129; hg19: chr4-56668431;