ENST00000520582.2:n.654-3667G>A

Variant names:

• chr8-8957380-G-A
• rs11778913
• ENST00000520582.2:n.654-3667G>A

Variant summary

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

The ENST00000520582.2(ENSG00000293372):​n.654-3667G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 152,100 control chromosomes in the GnomAD database, including 43,305 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 0.75 (43305 hom., cov: 31)
• Consequence: ENSG00000293372 ENST00000520582.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.595
• Publications: 4 publications found

Genes affected

ENSG00000293372 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.804 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
ENSG00000293372	ENST00000520582.2	n.654-3667G>A		intron_variant	Intron 5 of 7	3
ENSG00000293372	ENST00000753008.1	n.614+21590G>A		intron_variant	Intron 4 of 4
ENSG00000293372	ENST00000753009.1	n.428-21617G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114437 AN: 151982 Hom.: 43262 Cov.: 31

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.753 AC: 114538 AN: 152100 Hom.: 43305 Cov.: 31 AF XY: 0.756 AC XY: 56191 AN XY: 74350

African (AFR) AF: 0.749 AC: 31069 AN: 41488

American (AMR) AF: 0.816 AC: 12472 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2131 AN: 3470

East Asian (EAS) AF: 0.751 AC: 3882 AN: 5166

South Asian (SAS) AF: 0.662 AC: 3190 AN: 4818

European-Finnish (FIN) AF: 0.779 AC: 8261 AN: 10598

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51026 AN: 67966

Other (OTH) AF: 0.734 AC: 1547 AN: 2108

Alfa AF: 0.746 Hom.: 180643

Bravo AF: 0.757

Asia WGS AF: 0.681 AC: 2366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.9
DANN	Benign	0.65
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs11778913; hg19: chr8-8814890;