Genetic Variant ENSG00000254194:n.228+3513G>A (chr8-34006009-C-T) – 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 ENST00000518163.6(ENSG00000254194):n.228+3513G>A variant causes a intron 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: 29)

Consequence

ENSG00000254194
ENST00000518163.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.364

Publications

4 publications found

Variant links:

Genes affected

ENSG00000254194 (HGNC:):

ENSG00000254194 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=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105379364	NR_189605.1 link	n.746-28877C>T	intron_variant	Intron 3 of 11
LOC105379364	NR_189606.1 link	n.331-1847C>T	intron_variant	Intron 2 of 9
LOC105379364	NR_189607.1 link	n.331-127580C>T	intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000254194	ENST00000518163.6 link	n.228+3513G>A	intron_variant	Intron 3 of 4	3
ENSG00000253642	ENST00000521541.2 link	n.314-1847C>T	intron_variant	Intron 2 of 3	2
ENSG00000254194	ENST00000521714.1 link	n.75-673G>A	intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.0

(source)

DANN

Benign

0.74

PhyloP100

-0.36

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

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over