Genetic Variant APOM:c.114+16G>T (chr6-31656096-G-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 NM_019101.3(APOM):c.114+16G>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)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

APOM
NM_019101.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.192

Publications

0 publications found

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]

APOM 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=-0.73).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
APOM	NM_019101.3 link	c.114+16G>T	intron_variant	Intron 1 of 5	ENST00000375916.4	NP_061974.2
APOM	NM_001256169.2 link	c.-102-376G>T	intron_variant	Intron 1 of 5		NP_001243098.1
APOM	NR_045828.2 link	n.149-376G>T	intron_variant	Intron 1 of 5
APOM	XM_006715150.4 link	c.11+16G>T	intron_variant	Intron 1 of 5		XP_006715213.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
APOM	ENST00000375916.4 link	c.114+16G>T	intron_variant	Intron 1 of 5	1	NM_019101.3	ENSP00000365081.3
APOM	ENST00000375920.8 link	c.-102-376G>T	intron_variant	Intron 1 of 5	1		ENSP00000365085.4
APOM	ENST00000375918.6 link	c.-102-376G>T	intron_variant	Intron 1 of 4	2		ENSP00000365083.2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1394846

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

688876

African (AFR)

AF:

0.00

AC:

AN:

31794

American (AMR)

AF:

0.00

AC:

AN:

35970

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25258

East Asian (EAS)

AF:

0.00

AC:

AN:

36280

South Asian (SAS)

AF:

0.00

AC:

AN:

79398

European-Finnish (FIN)

AF:

0.00

AC:

AN:

48604

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5352

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1074176

Other (OTH)

AF:

0.00

AC:

AN:

58014

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

0.19

PromoterAI

-0.025

Neutral

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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