GeneBe

rs2964475

Variant names:

Variant summary

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

The ENST00000669435.2(ENSG00000286753):​n.817+13050A>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: 32)

Consequence

ENSG00000286753
ENST00000669435.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.220
Variant links:
Genes affected

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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=-0.95).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC101929200XR_001742583.3 linkn.817+13050A>T intron_variant Intron 2 of 5
LOC101929200XR_001742584.3 linkn.817+13050A>T intron_variant Intron 2 of 3
LOC101929200XR_007059118.1 linkn.817+13050A>T intron_variant Intron 2 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000286753ENST00000669435.2 linkn.817+13050A>T intron_variant Intron 2 of 2
ENSG00000286753ENST00000686499.1 linkn.817+13050A>T intron_variant Intron 2 of 3
ENSG00000286753ENST00000690642.1 linkn.903+10324A>T intron_variant Intron 3 of 4
ENSG00000286753ENST00000693678.1 linkn.329+13050A>T intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.8
DANN
Benign
0.30

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-5407814; API