6-31656096-G-C

Variant summary

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

The NM_019101.3(APOM):​c.114+16G>C 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

APOM
NM_019101.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.192
Variant links:
Genes affected
APOM (HGNC:13916): (apolipoprotein M) The protein encoded by this gene is an apolipoprotein and member of the lipocalin protein family. It is found associated with high density lipoproteins and to a lesser extent with low density lipoproteins and triglyceride-rich lipoproteins. The encoded protein is secreted through the plasma membrane but remains membrane-bound, where it is involved in lipid transport. Alternate splicing results in both coding and non-coding variants of this gene. [provided by RefSeq, Jan 2012]

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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=-0.74).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
APOMNM_019101.3 linkc.114+16G>C intron_variant Intron 1 of 5 ENST00000375916.4 NP_061974.2 O95445-1
APOMNM_001256169.2 linkc.-102-376G>C intron_variant Intron 1 of 5 NP_001243098.1 O95445-2A0A1U9X793
APOMXM_006715150.4 linkc.11+16G>C intron_variant Intron 1 of 5 XP_006715213.1
APOMNR_045828.2 linkn.149-376G>C intron_variant Intron 1 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
APOMENST00000375916.4 linkc.114+16G>C intron_variant Intron 1 of 5 1 NM_019101.3 ENSP00000365081.3 O95445-1
APOMENST00000375920.8 linkc.-102-376G>C intron_variant Intron 1 of 5 1 ENSP00000365085.4 O95445-2
APOMENST00000375918.6 linkc.-102-376G>C intron_variant Intron 1 of 4 2 ENSP00000365083.2 Q5SRP5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
28
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
12
DANN
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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: chr6-31623873; API