chr2-55820972-G-C

Position:

• chr2-55820972-G-C

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 0.2 in 152,090 control chromosomes in the GnomAD database, including 4,146 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 0.20 (4146 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.55820972G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30355 AN: 151970 Hom.: 4147 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.200 AC: 30365 AN: 152090 Hom.: 4146 Cov.: 33 AF XY: 0.204 AC XY: 15177 AN XY: 74350

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.211

Alfa AF: 0.108 Hom.: 172

Bravo AF: 0.200

Asia WGS AF: 0.480 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6730839; hg19: chr2-56048107;