8-5603316-C-A

Variant names:

• chr8-5603316-C-A
• rs2408007
• ENST00000807442.1:n.228+781G>T

Variant summary

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

The ENST00000807442.1(ENSG00000304969):​n.228+781G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,206 control chromosomes in the GnomAD database, including 3,709 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 0.21 (3709 hom., cov: 29)
• Consequence: ENSG00000304969 ENST00000807442.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 publications found

Genes affected

ENSG00000304969 (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 (EAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807442.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304969	ENST00000807442.1		n.228+781G>T		intron	N/A
	ENSG00000304969	ENST00000807443.1		n.229+781G>T		intron	N/A
	ENSG00000304969	ENST00000807444.1		n.211+781G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31766 AN: 151090 Hom.: 3708 Cov.: 29

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.210 AC: 31779 AN: 151206 Hom.: 3709 Cov.: 29 AF XY: 0.207 AC XY: 15296 AN XY: 73804

African (AFR) AF: 0.105 AC: 4307 AN: 41170

American (AMR) AF: 0.218 AC: 3302 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 917 AN: 3466

East Asian (EAS) AF: 0.281 AC: 1427 AN: 5076

South Asian (SAS) AF: 0.187 AC: 895 AN: 4782

European-Finnish (FIN) AF: 0.230 AC: 2381 AN: 10370

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17777 AN: 67876

Other (OTH) AF: 0.215 AC: 451 AN: 2102

Alfa AF: 0.243 Hom.: 14074

Bravo AF: 0.208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2408007; hg19: chr8-5460838;