ENST00000691186.2:n.282-7505A>G

Variant names:

• chr3-30461528-A-G
• rs4613502
• ENST00000691186.2:n.282-7505A>G

Variant summary

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

The ENST00000691186.2(ENSG00000289450):​n.282-7505A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,978 control chromosomes in the GnomAD database, including 32,816 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 0.64 (32816 hom., cov: 32)
• Consequence: ENSG00000289450 ENST00000691186.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 2 publications found

Genes affected

ENSG00000289450 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691186.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289450	ENST00000691186.2		n.282-7505A>G		intron	N/A
	ENSG00000227549	ENST00000813769.1		n.398+5585T>C		intron	N/A
	ENSG00000289450	ENST00000813894.1		n.392-7505A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96465 AN: 151858 Hom.: 32762 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.636 AC: 96585 AN: 151978 Hom.: 32816 Cov.: 32 AF XY: 0.638 AC XY: 47384 AN XY: 74280

African (AFR) AF: 0.865 AC: 35861 AN: 41474

American (AMR) AF: 0.536 AC: 8182 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1850 AN: 3464

East Asian (EAS) AF: 0.916 AC: 4733 AN: 5166

South Asian (SAS) AF: 0.752 AC: 3621 AN: 4818

European-Finnish (FIN) AF: 0.537 AC: 5675 AN: 10564

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34810 AN: 67930

Other (OTH) AF: 0.596 AC: 1253 AN: 2104

Alfa AF: 0.554 Hom.: 31315

Bravo AF: 0.645

Asia WGS AF: 0.817 AC: 2841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.31
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs4613502; hg19: chr3-30503020;