ENST00000791650.1:n.359C>A

Variant names:

• chr10-44398995-C-A
• rs1779384
• ENST00000791650.1:n.359C>A

Variant summary

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

The ENST00000791650.1(ENSG00000303087):​n.359C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,874 control chromosomes in the GnomAD database, including 4,524 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 0.24 (4524 hom., cov: 32)
• Consequence: ENSG00000303087 ENST00000791650.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689
• Publications: 6 publications found

Genes affected

ENSG00000303087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791650.1. 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
	ENSG00000303087	ENST00000791650.1		n.359C>A		non_coding_transcript_exon	Exon 3 of 5

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36285 AN: 151758 Hom.: 4512 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.239 AC: 36323 AN: 151874 Hom.: 4524 Cov.: 32 AF XY: 0.237 AC XY: 17559 AN XY: 74226

African (AFR) AF: 0.303 AC: 12542 AN: 41420

American (AMR) AF: 0.185 AC: 2822 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3466

East Asian (EAS) AF: 0.315 AC: 1611 AN: 5118

South Asian (SAS) AF: 0.269 AC: 1291 AN: 4798

European-Finnish (FIN) AF: 0.203 AC: 2142 AN: 10558

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14129 AN: 67946

Other (OTH) AF: 0.215 AC: 455 AN: 2112

Alfa AF: 0.212 Hom.: 6047

Bravo AF: 0.240

Asia WGS AF: 0.249 AC: 863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.34
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs1779384; hg19: chr10-44894443;