ENST00000789355.1:n.284T>C

Variant names:

• chr17-39867492-A-G
• rs4795397
• ENST00000789355.1:n.284T>C

Variant summary

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

The ENST00000789355.1(ENSG00000302760):​n.284T>C 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 0.384 in 151,136 control chromosomes in the GnomAD database, including 12,104 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 0.38 (12104 hom., cov: 31)
• Consequence: ENSG00000302760 ENST00000789355.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 49 publications found

Genes affected

ENSG00000302760 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789355.1. 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
	ENSG00000302760	ENST00000789355.1		n.284T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58006 AN: 151016 Hom.: 12091 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.368

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.384 AC: 58045 AN: 151136 Hom.: 12104 Cov.: 31 AF XY: 0.387 AC XY: 28624 AN XY: 73906

African (AFR) AF: 0.220 AC: 9121 AN: 41384

American (AMR) AF: 0.389 AC: 5895 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1559 AN: 3450

East Asian (EAS) AF: 0.271 AC: 1402 AN: 5164

South Asian (SAS) AF: 0.374 AC: 1804 AN: 4820

European-Finnish (FIN) AF: 0.534 AC: 5636 AN: 10564

Middle Eastern (MID) AF: 0.361 AC: 104 AN: 288

European-Non Finnish (NFE) AF: 0.462 AC: 31133 AN: 67324

Other (OTH) AF: 0.373 AC: 784 AN: 2104

Alfa AF: 0.330 Hom.: 2519

Bravo AF: 0.357

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.34
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs4795397; hg19: chr17-38023745;