rs3117581

chr6-31657087-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019101.3(APOM):c.270-138A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.085 in 756,386 control chromosomes in the GnomAD database, including 3,913 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 0.073 (524 hom., cov: 31)
  • Exomes 𝑓: 0.088 (3389 hom.)
• Consequence: APOM NM_019101.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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	UniProt
APOM	NM_019101.3	c.270-138A>G		intron_variant		ENST00000375916.4
APOM	NM_001256169.2	c.54-138A>G		intron_variant
APOM	XM_006715150.4	c.174-138A>G		intron_variant
APOM	NR_045828.2	n.311-138A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOM	ENST00000375916.4	c.270-138A>G		intron_variant		1	NM_019101.3	P1
APOM	ENST00000375920.8	c.54-138A>G		intron_variant		1
APOM	ENST00000375918.6	c.54-138A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0726 AC: 11016 AN: 151778 Hom.: 524 Cov.: 31

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00125

Gnomad FIN AF: 0.0788

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0548

GnomAD4 exome AF: 0.0881 AC: 53274 AN: 604492 Hom.: 3389 AF XY: 0.0842 AC XY: 26607 AN XY: 316008

Gnomad4 AFR exome AF: 0.0514

Gnomad4 AMR exome AF: 0.0260

Gnomad4 ASJ exome AF: 0.0418

Gnomad4 EAS exome AF: 0.0000614

Gnomad4 SAS exome AF: 0.00274

Gnomad4 FIN exome AF: 0.0834

Gnomad4 NFE exome AF: 0.115

Gnomad4 OTH exome AF: 0.0812

GnomAD4 genome AF: 0.0725 AC: 11016 AN: 151894 Hom.: 524 Cov.: 31 AF XY: 0.0676 AC XY: 5021 AN XY: 74244

Gnomad4 AFR AF: 0.0484

Gnomad4 AMR AF: 0.0352

Gnomad4 ASJ AF: 0.0398

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00125

Gnomad4 FIN AF: 0.0788

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0542

Alfa AF: 0.0964 Hom.: 96

Bravo AF: 0.0688

Asia WGS AF: 0.00837 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.8
Dann	Benign	0.56

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

Other links and lift over

dbSNP: rs3117581; hg19: chr6-31624864;