Genetic Variant ENSG00000288109:n.493C>G (chr17-67717234-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000832642.1(ENSG00000288109):n.493C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Consequence

ENSG00000288109
ENST00000832642.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.286

Publications

2 publications found

Variant links:

Genes affected

ENSG00000288109 (HGNC:):

ENSG00000288109 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832642.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
LOC101928045	NR_188292.1	n.185+260C>G	intron	N/A
LOC101928045	NR_188293.1	n.37+408C>G	intron	N/A
LOC101928045	NR_188294.1	n.37+408C>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000288109	ENST00000832642.1	n.493C>G	non_coding_transcript_exon	Exon 1 of 1
ENSG00000288109	ENST00000832617.1	n.198-27861C>G	intron	N/A
ENSG00000288109	ENST00000832618.1	n.212-27861C>G	intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

94143

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.1

(source)

DANN

Benign

0.50

PhyloP100

-0.29

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over