1-55034756-A-G

Variant names:

• chr1-55034756-A-G
• rs2182833

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 0.24 in 152,172 control chromosomes in the GnomAD database, including 5,259 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 (5259 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 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: 0.240 AC: 36432 AN: 152054 Hom.: 5240 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.240 AC: 36497 AN: 152172 Hom.: 5259 Cov.: 33 AF XY: 0.239 AC XY: 17810 AN XY: 74424

African (AFR) AF: 0.290 AC: 12029 AN: 41510

American (AMR) AF: 0.295 AC: 4509 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3468

East Asian (EAS) AF: 0.653 AC: 3375 AN: 5172

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4824

European-Finnish (FIN) AF: 0.104 AC: 1105 AN: 10596

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12744 AN: 68000

Other (OTH) AF: 0.265 AC: 559 AN: 2108

Alfa AF: 0.212 Hom.: 17217

Bravo AF: 0.259

Asia WGS AF: 0.418 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.86
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs2182833; hg19: chr1-55500429;