ENST00000688917.2:n.428C>T

Variant names:

• chr18-9102142-G-A
• rs1156044
• ENST00000688917.2:n.428C>T

Variant summary

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

The ENST00000688917.2(ENSG00000288939):​n.428C>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 0.816 in 151,984 control chromosomes in the GnomAD database, including 50,705 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 0.82 (50705 hom., cov: 29)
• Consequence: ENSG00000288939 ENST00000688917.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 9 publications found

Genes affected

ENSG00000288939 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688917.2. 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
	ENSG00000288939	ENST00000688917.2		n.428C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000288939	ENST00000827765.1		n.123+262C>T		intron	N/A
	ENSG00000288939	ENST00000827767.1		n.100+262C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.816 AC: 123913 AN: 151866 Hom.: 50659 Cov.: 29

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.816 AC: 124012 AN: 151984 Hom.: 50705 Cov.: 29 AF XY: 0.813 AC XY: 60377 AN XY: 74282

African (AFR) AF: 0.797 AC: 33021 AN: 41422

American (AMR) AF: 0.774 AC: 11832 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3167 AN: 3472

East Asian (EAS) AF: 0.731 AC: 3776 AN: 5168

South Asian (SAS) AF: 0.863 AC: 4147 AN: 4806

European-Finnish (FIN) AF: 0.779 AC: 8211 AN: 10544

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57054 AN: 67970

Other (OTH) AF: 0.833 AC: 1763 AN: 2116

Alfa AF: 0.834 Hom.: 75660

Bravo AF: 0.814

Asia WGS AF: 0.750 AC: 2607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.79
DANN	Benign	0.72
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1156044; hg19: chr18-9102140;