8-110273886-C-G

Variant names:

• chr8-110273886-C-G
• rs3019325
• ENST00000817559.1:n.320+10757C>G

Variant summary

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

The ENST00000817559.1(ENSG00000306390):​n.320+10757C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,028 control chromosomes in the GnomAD database, including 42,527 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 0.74 (42527 hom., cov: 31)
• Consequence: ENSG00000306390 ENST00000817559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 1 publications found

Genes affected

ENSG00000306390 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000817559.1. 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
	ENSG00000306390	ENST00000817559.1		n.320+10757C>G		intron	N/A
	ENSG00000306390	ENST00000817562.1		n.268+10757C>G		intron	N/A
	ENSG00000306390	ENST00000817563.1		n.269-4186C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112399 AN: 151910 Hom.: 42479 Cov.: 31

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.740 AC: 112503 AN: 152028 Hom.: 42527 Cov.: 31 AF XY: 0.738 AC XY: 54846 AN XY: 74312

African (AFR) AF: 0.883 AC: 36646 AN: 41510

American (AMR) AF: 0.620 AC: 9479 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2321 AN: 3466

East Asian (EAS) AF: 0.847 AC: 4366 AN: 5156

South Asian (SAS) AF: 0.744 AC: 3590 AN: 4828

European-Finnish (FIN) AF: 0.703 AC: 7426 AN: 10560

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46476 AN: 67914

Other (OTH) AF: 0.697 AC: 1473 AN: 2114

Alfa AF: 0.722 Hom.: 4712

Bravo AF: 0.735

Asia WGS AF: 0.794 AC: 2754 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.25
PhyloP100		-0.063

Splicing

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

Other links and lift over

dbSNP: rs3019325; hg19: chr8-111286115;