Variant 6-31652743-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000375920.8(APOM):c.-103+192T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 153,158 control chromosomes in the GnomAD database, including 513 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 0.069 ( 508 hom., cov: 32)

Exomes 𝑓: 0.054 ( 5 hom. )

Consequence

APOM
ENST00000375920.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0270

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:

BAG6 (HGNC:13919): (BAG cochaperone 6) This gene was first characterized as part of a cluster of genes located within the human major histocompatibility complex class III region. This gene encodes a nuclear protein that is cleaved by caspase 3 and is implicated in the control of apoptosis. In addition, the protein forms a complex with E1A binding protein p300 and is required for the acetylation of p53 in response to DNA damage. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

BAG6 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 (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOM	NM_001256169.2 linkuse as main transcript	c.-103+192T>G		intron_variant			NP_001243098.1
APOM	NR_045828.2 linkuse as main transcript	n.148+192T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	Appris	UniProt
APOM	ENST00000375920.8 linkuse as main transcript	c.-103+192T>G	intron_variant	1	ENSP00000365085		O95445-2
APOM	ENST00000375918.6 linkuse as main transcript	c.-103+192T>G	intron_variant	2	ENSP00000365083
BAG6	ENST00000211379.9 linkuse as main transcript		upstream_gene_variant	1	ENSP00000211379	P2	P46379-2

Frequencies

GnomAD3 genomes

AF:

0.0694

AC:

10559

AN:

152098

Hom.:

508

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0388

Gnomad AMI

AF:

0.0692

Gnomad AMR

AF:

0.0316

Gnomad ASJ

AF:

0.0397

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.0784

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.0516

GnomAD4 exome

AF:

0.0541

AC:

AN:

942

Hom.:

Cov.:

AF XY:

0.0529

AC XY:

AN XY:

586

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0893

Gnomad4 NFE exome

AF:

0.0712

Gnomad4 OTH exome

AF:

0.0641

GnomAD4 genome

AF:

0.0694

AC:

10558

AN:

152216

Hom.:

508

Cov.:

AF XY:

0.0647

AC XY:

4818

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0387

Gnomad4 AMR

AF:

0.0315

Gnomad4 ASJ

AF:

0.0397

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0784

Gnomad4 NFE

AF:

0.108

Gnomad4 OTH

AF:

0.0511

Alfa

AF:

0.0964

Hom.:

1453

Bravo

AF:

0.0650

Asia WGS

AF:

0.00693

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

2.9

DANN

Benign

0.77

Splicing

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