ENST00000815627.1:n.471+13393G>A

Variant names:

• chr4-20235227-C-T
• rs574666
• ENST00000815627.1:n.471+13393G>A

Variant summary

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

The ENST00000815627.1(ENSG00000306143):​n.471+13393G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,040 control chromosomes in the GnomAD database, including 35,785 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 0.68 (35785 hom., cov: 32)
• Consequence: ENSG00000306143 ENST00000815627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 2 publications found

Genes affected

ENSG00000306143 (HGNC:58754):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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
ENSG00000306143	ENST00000815627.1	n.471+13393G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103611 AN: 151922 Hom.: 35774 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.682 AC: 103659 AN: 152040 Hom.: 35785 Cov.: 32 AF XY: 0.688 AC XY: 51149 AN XY: 74324

African (AFR) AF: 0.596 AC: 24691 AN: 41462

American (AMR) AF: 0.786 AC: 12016 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2758 AN: 3470

East Asian (EAS) AF: 0.972 AC: 5008 AN: 5152

South Asian (SAS) AF: 0.791 AC: 3804 AN: 4812

European-Finnish (FIN) AF: 0.665 AC: 7033 AN: 10568

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.677 AC: 46021 AN: 67980

Other (OTH) AF: 0.718 AC: 1517 AN: 2114

Alfa AF: 0.673 Hom.: 4626

Bravo AF: 0.690

Asia WGS AF: 0.858 AC: 2982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.73
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs574666; hg19: chr4-20236850; COSMIC: COSV53465233;