rs4832712

Variant names:

• chr2-17175118-A-G
• rs4832712
• ENST00000845015.1:n.253+18246T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-17175118-A-G
• chr2-17175118-A-T

Variant summary

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

The ENST00000845015.1(ENSG00000309887):​n.253+18246T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,140 control chromosomes in the GnomAD database, including 2,442 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 0.11 (2442 hom., cov: 32)
• Consequence: ENSG00000309887 ENST00000845015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 0 publications found

Genes affected

ENSG00000309887 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000845015.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309887	ENST00000845015.1		n.253+18246T>C		intron	N/A
	ENSG00000309902	ENST00000845391.1		n.125+2633A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17251 AN: 152022 Hom.: 2433 Cov.: 32

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0546

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.114 AC: 17282 AN: 152140 Hom.: 2442 Cov.: 32 AF XY: 0.125 AC XY: 9316 AN XY: 74368

African (AFR) AF: 0.0793 AC: 3294 AN: 41532

American (AMR) AF: 0.183 AC: 2789 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0438 AC: 152 AN: 3468

East Asian (EAS) AF: 0.767 AC: 3928 AN: 5124

South Asian (SAS) AF: 0.227 AC: 1094 AN: 4810

European-Finnish (FIN) AF: 0.186 AC: 1970 AN: 10598

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0547 AC: 3719 AN: 68014

Other (OTH) AF: 0.140 AC: 296 AN: 2114

Alfa AF: 0.0802 Hom.: 107

Bravo AF: 0.115

Asia WGS AF: 0.490 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.44
DANN	Benign	0.57
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs4832712; hg19: chr2-17356385;