dbSNP rs2130604: ENSG00000286215:n.3037-1890A>T (chr6-126499415-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000650727.1(ENSG00000286215):n.3037-1890A>T 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: 31)

Consequence

ENSG00000286215
ENST00000650727.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.755

Variant links:

Genes affected

ENSG00000286215 (HGNC:):

ENSG00000286215 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286215	ENST00000650727.1 link	n.3037-1890A>T	intron_variant	Intron 14 of 14
ENSG00000286215	ENST00000651326.1 link	n.2290-26821A>T	intron_variant	Intron 5 of 6
ENSG00000286215	ENST00000652383.1 link	n.630+32248A>T	intron_variant	Intron 3 of 4
ENSG00000286215	ENST00000652545.1 link	n.3347-1890A>T	intron_variant	Intron 15 of 15

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

-0.93

CADD

Benign

0.72

DANN

Benign

0.33

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over