Variant 6-31657730-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019101.3(APOM):c.541+7G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0739 in 1,606,622 control chromosomes in the GnomAD database, including 8,216 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 2549 hom., cov: 32)

Exomes 𝑓: 0.067 ( 5667 hom. )

Consequence

APOM
NM_019101.3 splice_region, intron

Scores

Splicing: ADA: 0.00001998

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.862

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:

APOM (HGNC:):

APOM links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0012431145).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
APOM	NM_019101.3 linkuse as main transcript	c.541+7G>T	splice_region_variant, intron_variant	ENST00000375916.4	NP_061974.2	O95445-1
APOM	NM_001256169.2 linkuse as main transcript	c.325+7G>T	splice_region_variant, intron_variant		NP_001243098.1	O95445-2A0A1U9X793
APOM	XM_006715150.4 linkuse as main transcript	c.445+7G>T	splice_region_variant, intron_variant		XP_006715213.1
APOM	NR_045828.2 linkuse as main transcript	n.582+7G>T	splice_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
APOM	ENST00000375916.4 linkuse as main transcript	c.541+7G>T		splice_region_variant, intron_variant		1	NM_019101.3	ENSP00000365081.3	O95445-1
APOM	ENST00000375920.8 linkuse as main transcript	c.325+7G>T		splice_region_variant, intron_variant		1		ENSP00000365085.4	O95445-2
APOM	ENST00000375918.6 linkuse as main transcript	c.332G>T	p.Gly111Val	missense_variant	5/5	2		ENSP00000365083.2	Q5SRP5

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21322

AN:

151976

Hom.:

2539

Cov.:

show subpopulations

Gnomad AFR

AF:

0.317

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.0814

Gnomad FIN

AF:

0.00680

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.0550

Gnomad OTH

AF:

0.176

GnomAD3 exomes

AF:

0.0931

AC:

23033

AN:

247410

Hom.:

1920

AF XY:

0.0868

AC XY:

11683

AN XY:

134586

show subpopulations

Gnomad AFR exome

AF:

0.321

Gnomad AMR exome

AF:

0.127

Gnomad ASJ exome

AF:

0.192

Gnomad EAS exome

AF:

0.160

Gnomad SAS exome

AF:

0.0726

Gnomad FIN exome

AF:

0.00634

Gnomad NFE exome

AF:

0.0534

Gnomad OTH exome

AF:

0.104

GnomAD4 exome

AF:

0.0669

AC:

97355

AN:

1454528

Hom.:

5667

Cov.:

AF XY:

0.0664

AC XY:

48081

AN XY:

724102

show subpopulations

Gnomad4 AFR exome

AF:

0.326

Gnomad4 AMR exome

AF:

0.130

Gnomad4 ASJ exome

AF:

0.193

Gnomad4 EAS exome

AF:

0.151

Gnomad4 SAS exome

AF:

0.0728

Gnomad4 FIN exome

AF:

0.00801

Gnomad4 NFE exome

AF:

0.0504

Gnomad4 OTH exome

AF:

0.0987

GnomAD4 genome

AF:

0.140

AC:

21355

AN:

152094

Hom.:

2549

Cov.:

AF XY:

0.138

AC XY:

10267

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.317

Gnomad4 AMR

AF:

0.137

Gnomad4 ASJ

AF:

0.192

Gnomad4 EAS

AF:

0.154

Gnomad4 SAS

AF:

0.0808

Gnomad4 FIN

AF:

0.00680

Gnomad4 NFE

AF:

0.0550

Gnomad4 OTH

AF:

0.176

Alfa

AF:

0.0991

Hom.:

1000

Bravo

AF:

0.159

TwinsUK

AF:

0.0472

AC:

175

ALSPAC

AF:

0.0488

AC:

188

ESP6500AA

AF:

0.306

AC:

925

ESP6500EA

AF:

0.0596

AC:

323

ExAC

AF:

0.0913

AC:

10982

Asia WGS

AF:

0.122

AC:

425

AN:

3478

EpiCase

AF:

0.0667

EpiControl

AF:

0.0695

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.42

CADD

Benign

7.1

DANN

Benign

0.67

DEOGEN2

Benign

0.022

Eigen

Benign

0.18

Eigen_PC

Benign

-0.063

FATHMM_MKL

Benign

0.52

MetaRNN

Benign

0.0012

MetaSVM

Benign

-0.96

PROVEAN

Benign

0.82

REVEL

Benign

0.019

Sift

Pathogenic

0.0

Vest4

0.087

ClinPred

0.065

GERP RS

2.7

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000020

dbscSNV1_RF

Benign

0.010

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

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