rs2156107

Positions:

• chr18-72879235-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_134648.1(NETO1-DT):​n.76-1955C>T variant causes a intron, non coding transcript 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 NR_134648.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NETO1-DT	NR_134648.1	n.76-1955C>T		intron_variant, non_coding_transcript_variant
NETO1-DT	NR_134647.1	n.102-852C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NETO1-DT	ENST00000580564.1	n.76-1955C>T		intron_variant, non_coding_transcript_variant		5
NETO1-DT	ENST00000664848.1	n.1792C>T		non_coding_transcript_exon_variant	1/2
NETO1-DT	ENST00000578967.3	n.205-852C>T		intron_variant, non_coding_transcript_variant		2
NETO1-DT	ENST00000687839.2	n.206-1955C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.937

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.962

Gnomad4 OTH AF: 0.904

Alfa AF: 0.946 Hom.: 65364

Bravo AF: 0.879

Asia WGS AF: 0.808 AC: 2809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2156107; hg19: chr18-70546470;