rs17039212

Variant names:

• chr2-49728359-C-A
• rs17039212

Your query was ambiguous. Multiple possible variants found:

• chr2-49728359-C-A
• chr2-49728359-C-G

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 0.144 in 152,140 control chromosomes in the GnomAD database, including 1,864 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 0.14 (1864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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: 0.144 AC: 21928 AN: 152022 Hom.: 1856 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.144 AC: 21953 AN: 152140 Hom.: 1864 Cov.: 32 AF XY: 0.147 AC XY: 10920 AN XY: 74352

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.142

Alfa AF: 0.110 Hom.: 2040

Bravo AF: 0.156

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17039212; hg19: chr2-49955497;