ENST00000830399.1:n.180+18336A>G

Variant names:

• chr4-114746031-A-G
• rs4833467
• ENST00000830399.1:n.180+18336A>G

Variant summary

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

The ENST00000830399.1(ENSG00000308009):​n.180+18336A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,922 control chromosomes in the GnomAD database, including 32,195 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 (32195 hom., cov: 30)
• Consequence: ENSG00000308009 ENST00000830399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 1 publications found

Genes affected

ENSG00000308009 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 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
ENSG00000308009	ENST00000830399.1	n.180+18336A>G		intron_variant	Intron 1 of 2
ENSG00000308009	ENST00000830400.1	n.172+18336A>G		intron_variant	Intron 1 of 1
ENSG00000308009	ENST00000830401.1	n.200+18336A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97592 AN: 151804 Hom.: 32138 Cov.: 30

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.643 AC: 97712 AN: 151922 Hom.: 32195 Cov.: 30 AF XY: 0.648 AC XY: 48139 AN XY: 74242

African (AFR) AF: 0.769 AC: 31867 AN: 41464

American (AMR) AF: 0.638 AC: 9724 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1649 AN: 3470

East Asian (EAS) AF: 0.819 AC: 4212 AN: 5142

South Asian (SAS) AF: 0.716 AC: 3447 AN: 4812

European-Finnish (FIN) AF: 0.596 AC: 6299 AN: 10560

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38516 AN: 67918

Other (OTH) AF: 0.627 AC: 1319 AN: 2104

Alfa AF: 0.577 Hom.: 49063

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.54
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4833467; hg19: chr4-115667187;