2-55622174-A-G

Position:

• chr2-55622174-A-G

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 0.434 in 152,112 control chromosomes in the GnomAD database, including 15,252 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 0.43 (15252 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.55622174A>G		intergenic_region
PPP4R3B-DT	NR_186621.1	n.454-3547A>G		intron_variant
PPP4R3B-DT	NR_186622.1	n.453+3792A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.434 AC: 66011 AN: 151994 Hom.: 15253 Cov.: 33

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.434 AC: 66030 AN: 152112 Hom.: 15252 Cov.: 33 AF XY: 0.432 AC XY: 32142 AN XY: 74370

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.462

Alfa AF: 0.486 Hom.: 19254

Bravo AF: 0.424

Asia WGS AF: 0.230 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs782602; hg19: chr2-55849309;