ENST00000794042.1:n.183+3030C>A

Variant names:

• chr8-59266162-C-A
• rs10089517
• ENST00000794042.1:n.183+3030C>A

Variant summary

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

The ENST00000794042.1(ENSG00000303378):​n.183+3030C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,872 control chromosomes in the GnomAD database, including 8,182 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 0.31 (8182 hom., cov: 32)
• Consequence: ENSG00000303378 ENST00000794042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 14 publications found

Genes affected

ENSG00000303378 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794042.1. 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
	ENSG00000303378	ENST00000794042.1		n.183+3030C>A		intron	N/A
	ENSG00000303378	ENST00000794043.1		n.280+3030C>A		intron	N/A
	ENSG00000303378	ENST00000794044.1		n.298+3030C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47607 AN: 151754 Hom.: 8179 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.314 AC: 47636 AN: 151872 Hom.: 8182 Cov.: 32 AF XY: 0.311 AC XY: 23097 AN XY: 74224

African (AFR) AF: 0.195 AC: 8074 AN: 41452

American (AMR) AF: 0.472 AC: 7195 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3464

East Asian (EAS) AF: 0.445 AC: 2293 AN: 5156

South Asian (SAS) AF: 0.240 AC: 1155 AN: 4816

European-Finnish (FIN) AF: 0.257 AC: 2693 AN: 10496

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23695 AN: 67926

Other (OTH) AF: 0.359 AC: 759 AN: 2112

Alfa AF: 0.348 Hom.: 27484

Bravo AF: 0.331

Asia WGS AF: 0.305 AC: 1053 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.1
DANN	Benign	0.34
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10089517; hg19: chr8-60178721;