rs17039212

Variant names:

• chr2-49728359-C-A
• rs17039212
• ENST00000809387.1:n.268-20233C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000809387.1(ENSG00000282828):​n.268-20233C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000282828 ENST00000809387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 9 publications found

Genes affected

ENSG00000282828 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000282828	ENST00000809387.1	n.268-20233C>A		intron_variant	Intron 2 of 5
ENSG00000282828	ENST00000809388.1	n.497-20233C>A		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.203 AC: 8433 AN: 41522

American (AMR) AF: 0.188 AC: 2870 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3468

East Asian (EAS) AF: 0.177 AC: 913 AN: 5158

South Asian (SAS) AF: 0.139 AC: 670 AN: 4808

European-Finnish (FIN) AF: 0.107 AC: 1137 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6907 AN: 68006

Other (OTH) AF: 0.142 AC: 301 AN: 2114

Alfa AF: 0.117 Hom.: 5127

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs17039212; hg19: chr2-49955497;