rs2918239

Variant names:

• chr3-115762715-A-C
• rs2918239
• ENST00000700882.2:n.237-4418T>G

Variant summary

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

The ENST00000700882.2(ENSG00000289153):​n.237-4418T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,126 control chromosomes in the GnomAD database, including 2,366 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 0.17 (2366 hom., cov: 32)
• Consequence: ENSG00000289153 ENST00000700882.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.92
• Publications: 4 publications found

Genes affected

ENSG00000289153 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000700882.2. 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
	ENSG00000289153	ENST00000700882.2		n.237-4418T>G		intron	N/A
	ENSG00000289153	ENST00000750609.1		n.208+29585T>G		intron	N/A
	ENSG00000289153	ENST00000750610.1		n.285-4418T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25672 AN: 152008 Hom.: 2353 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.169 AC: 25721 AN: 152126 Hom.: 2366 Cov.: 32 AF XY: 0.173 AC XY: 12862 AN XY: 74374

African (AFR) AF: 0.214 AC: 8885 AN: 41502

American (AMR) AF: 0.239 AC: 3645 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3470

East Asian (EAS) AF: 0.153 AC: 791 AN: 5176

South Asian (SAS) AF: 0.119 AC: 572 AN: 4818

European-Finnish (FIN) AF: 0.200 AC: 2112 AN: 10574

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8814 AN: 67988

Other (OTH) AF: 0.164 AC: 346 AN: 2110

Alfa AF: 0.164 Hom.: 435

Bravo AF: 0.171

Asia WGS AF: 0.137 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.4
DANN	Benign	0.69
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs2918239; hg19: chr3-115481562;