rs9267528

Variant names:

• chr6-31654364-C-T
• rs9267528
• ENST00000375920.8:c.-103+1813C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001256169.2(APOM):​c.-103+1813C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00582 in 152,194 control chromosomes in the GnomAD database, including 8 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 0.0058 (8 hom., cov: 32)
• Consequence: APOM NM_001256169.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BS2: High Homozygotes in GnomAd4 at 8 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256169.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOM	NM_001256169.2		c.-103+1813C>T		intron	N/A	NP_001243098.1	O95445-2
	APOM	NR_045828.2		n.148+1813C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOM	ENST00000375920.8	TSL:1	c.-103+1813C>T		intron	N/A	ENSP00000365085.4	O95445-2
	APOM	ENST00000375918.6	TSL:2	c.-103+1813C>T		intron	N/A	ENSP00000365083.2	Q5SRP5

Frequencies

GnomAD3 genomes AF: 0.00582 AC: 885 AN: 152076 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.00106

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.00694

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00768

Gnomad OTH AF: 0.00527

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00582 AC: 886 AN: 152194 Hom.: 8 Cov.: 32 AF XY: 0.00586 AC XY: 436 AN XY: 74424

African (AFR) AF: 0.00106 AC: 44 AN: 41494

American (AMR) AF: 0.00693 AC: 106 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.00186 AC: 9 AN: 4828

European-Finnish (FIN) AF: 0.0113 AC: 120 AN: 10598

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00768 AC: 522 AN: 67996

Other (OTH) AF: 0.00521 AC: 11 AN: 2110

Alfa AF: 0.00753 Hom.: 36

Bravo AF: 0.00544

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.1
DANN	Benign	0.83
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9267528; hg19: chr6-31622141;