ENST00000664848.1:n.1792C>T

Variant names:

• chr18-72879235-C-T
• rs2156107
• ENST00000664848.1:n.1792C>T

Variant summary

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

The ENST00000664848.1(NETO1-DT):​n.1792C>T 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 0.888 in 152,152 control chromosomes in the GnomAD database, including 60,650 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 0.89 (60650 hom., cov: 31)
• Consequence: NETO1-DT ENST00000664848.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 4 publications found

Genes affected

NETO1-DT (HGNC:55333): (NETO1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664848.1. 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
	NETO1-DT	NR_134647.1		n.102-852C>T		intron	N/A
	NETO1-DT	NR_134648.1		n.76-1955C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NETO1-DT	ENST00000664848.1		n.1792C>T		non_coding_transcript_exon	Exon 1 of 2
	NETO1-DT	ENST00000578967.4	TSL:2	n.271-852C>T		intron	N/A
	NETO1-DT	ENST00000580564.2	TSL:5	n.170-1955C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.888 AC: 135058 AN: 152034 Hom.: 60627 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.962

Gnomad OTH AF: 0.908

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

GnomAD4 genome AF: 0.888 AC: 135132 AN: 152152 Hom.: 60650 Cov.: 31 AF XY: 0.887 AC XY: 65975 AN XY: 74396

African (AFR) AF: 0.763 AC: 31641 AN: 41480

American (AMR) AF: 0.905 AC: 13842 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3252 AN: 3472

East Asian (EAS) AF: 0.668 AC: 3444 AN: 5154

South Asian (SAS) AF: 0.871 AC: 4195 AN: 4818

European-Finnish (FIN) AF: 0.968 AC: 10268 AN: 10612

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.962 AC: 65450 AN: 68010

Other (OTH) AF: 0.904 AC: 1911 AN: 2114

Alfa AF: 0.939 Hom.: 84292

Bravo AF: 0.879

Asia WGS AF: 0.808 AC: 2809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.74
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2156107; hg19: chr18-70546470;