Variant chr6-31657764-C-A 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+41C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0452 in 1,538,572 control chromosomes in the GnomAD database, including 3,093 homozygotes. 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: 𝑓 0.086 ( 956 hom., cov: 32)

Exomes 𝑓: 0.041 ( 2137 hom. )

Consequence

APOM
NM_019101.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.13

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
APOM	NM_019101.3 linkuse as main transcript	c.541+41C>A	intron_variant	ENST00000375916.4	NP_061974.2
APOM	NM_001256169.2 linkuse as main transcript	c.325+41C>A	intron_variant		NP_001243098.1
APOM	XM_006715150.4 linkuse as main transcript	c.445+41C>A	intron_variant		XP_006715213.1
APOM	NR_045828.2 linkuse as main transcript	n.582+41C>A	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOM	ENST00000375916.4 linkuse as main transcript	c.541+41C>A		intron_variant		1	NM_019101.3	ENSP00000365081	P1	O95445-1
APOM	ENST00000375920.8 linkuse as main transcript	c.325+41C>A		intron_variant		1		ENSP00000365085		O95445-2
APOM	ENST00000375918.6 linkuse as main transcript	c.366C>A	p.Thr122=	synonymous_variant	5/5	2		ENSP00000365083

Frequencies

GnomAD3 genomes

AF:

0.0862

AC:

13103

AN:

152022

Hom.:

956

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0765

Gnomad ASJ

AF:

0.0507

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.0626

Gnomad FIN

AF:

0.00481

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0312

Gnomad OTH

AF:

0.0955

GnomAD3 exomes

AF:

0.0570

AC:

14126

AN:

247858

Hom.:

813

AF XY:

0.0540

AC XY:

7265

AN XY:

134586

show subpopulations

Gnomad AFR exome

AF:

0.203

Gnomad AMR exome

AF:

0.0702

Gnomad ASJ exome

AF:

0.0495

Gnomad EAS exome

AF:

0.146

Gnomad SAS exome

AF:

0.0556

Gnomad FIN exome

AF:

0.00366

Gnomad NFE exome

AF:

0.0295

Gnomad OTH exome

AF:

0.0537

GnomAD4 exome

AF:

0.0407

AC:

56476

AN:

1386432

Hom.:

2137

Cov.:

AF XY:

0.0406

AC XY:

28167

AN XY:

694048

show subpopulations

Gnomad4 AFR exome

AF:

0.208

Gnomad4 AMR exome

AF:

0.0725

Gnomad4 ASJ exome

AF:

0.0519

Gnomad4 EAS exome

AF:

0.106

Gnomad4 SAS exome

AF:

0.0553

Gnomad4 FIN exome

AF:

0.00521

Gnomad4 NFE exome

AF:

0.0307

Gnomad4 OTH exome

AF:

0.0579

GnomAD4 genome

AF:

0.0862

AC:

13110

AN:

152140

Hom.:

956

Cov.:

AF XY:

0.0859

AC XY:

6387

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.201

Gnomad4 AMR

AF:

0.0764

Gnomad4 ASJ

AF:

0.0507

Gnomad4 EAS

AF:

0.137

Gnomad4 SAS

AF:

0.0624

Gnomad4 FIN

AF:

0.00481

Gnomad4 NFE

AF:

0.0312

Gnomad4 OTH

AF:

0.0964

Alfa

AF:

0.0491

Hom.:

625

Bravo

AF:

0.0967

Asia WGS

AF:

0.0920

AC:

318

AN:

3478

EpiCase

AF:

0.0358

EpiControl

AF:

0.0364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.72

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

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