2-55820972-G-C

Variant names:

• chr2-55820972-G-C
• rs6730839

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 0.2 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.124 AC: 5164 AN: 41506

American (AMR) AF: 0.198 AC: 3028 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3464

East Asian (EAS) AF: 0.800 AC: 4127 AN: 5160

South Asian (SAS) AF: 0.260 AC: 1252 AN: 4824

European-Finnish (FIN) AF: 0.183 AC: 1933 AN: 10580

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13296 AN: 67960

Other (OTH) AF: 0.211 AC: 445 AN: 2110

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
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs6730839; hg19: chr2-56048107;