rs1549582

Variant names:

• chr2-82461856-A-C
• rs1549582

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 0.37 in 151,838 control chromosomes in the GnomAD database, including 12,092 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 0.37 (12092 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 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: 0.370 AC: 56130 AN: 151722 Hom.: 12059 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.370 AC: 56212 AN: 151838 Hom.: 12092 Cov.: 32 AF XY: 0.362 AC XY: 26868 AN XY: 74168

African (AFR) AF: 0.587 AC: 24307 AN: 41404

American (AMR) AF: 0.275 AC: 4183 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1129 AN: 3468

East Asian (EAS) AF: 0.0288 AC: 149 AN: 5166

South Asian (SAS) AF: 0.196 AC: 948 AN: 4826

European-Finnish (FIN) AF: 0.265 AC: 2801 AN: 10558

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21616 AN: 67868

Other (OTH) AF: 0.329 AC: 694 AN: 2108

Alfa AF: 0.340 Hom.: 5107

Bravo AF: 0.379

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.41
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1549582; hg19: chr2-82688980;