rs17049480

Variant names:

• chr2-58354020-G-A
• rs17049480

Your query was ambiguous. Multiple possible variants found:

• chr2-58354020-G-A
• chr2-58354020-G-C

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 0.147 in 152,128 control chromosomes in the GnomAD database, including 1,911 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 0.15 (1911 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 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: 0.147 AC: 22343 AN: 152010 Hom.: 1912 Cov.: 32

Gnomad AFR AF: 0.0576

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.147 AC: 22351 AN: 152128 Hom.: 1911 Cov.: 32 AF XY: 0.149 AC XY: 11068 AN XY: 74362

African (AFR) AF: 0.0578 AC: 2400 AN: 41520

American (AMR) AF: 0.196 AC: 2997 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3472

East Asian (EAS) AF: 0.270 AC: 1399 AN: 5174

South Asian (SAS) AF: 0.243 AC: 1173 AN: 4820

European-Finnish (FIN) AF: 0.165 AC: 1749 AN: 10576

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.169 AC: 11474 AN: 67972

Other (OTH) AF: 0.187 AC: 394 AN: 2112

Alfa AF: 0.156 Hom.: 315

Bravo AF: 0.147

Asia WGS AF: 0.256 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	12
DANN	Benign	0.67
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs17049480; hg19: chr2-58581155;