ENST00000375920.8:c.-103+1715T>G

Variant names:

• chr6-31654266-T-G
• rs1266078
• ENST00000375920.8:c.-103+1715T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000375920.8(APOM):​c.-103+1715T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0842 in 148,078 control chromosomes in the GnomAD database, including 892 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 0.084 (892 hom., cov: 31)
• Consequence: APOM ENST00000375920.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783
• Publications: 11 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOM	NM_001256169.2	c.-103+1715T>G		intron_variant	Intron 1 of 5		NP_001243098.1
APOM	NR_045828.2	n.148+1715T>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOM	ENST00000375920.8	c.-103+1715T>G		intron_variant	Intron 1 of 5	1		ENSP00000365085.4
APOM	ENST00000375918.6	c.-103+1715T>G		intron_variant	Intron 1 of 4	2		ENSP00000365083.2

Frequencies

GnomAD3 genomes AF: 0.0842 AC: 12462 AN: 147964 Hom.: 891 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0166

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.0511

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0633

Gnomad FIN AF: 0.00548

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0314

Gnomad OTH AF: 0.0955

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

GnomAD4 genome AF: 0.0842 AC: 12468 AN: 148078 Hom.: 892 Cov.: 31 AF XY: 0.0839 AC XY: 6056 AN XY: 72164

African (AFR) AF: 0.196 AC: 7788 AN: 39810

American (AMR) AF: 0.0743 AC: 1103 AN: 14836

Ashkenazi Jewish (ASJ) AF: 0.0511 AC: 176 AN: 3444

East Asian (EAS) AF: 0.137 AC: 702 AN: 5108

South Asian (SAS) AF: 0.0631 AC: 297 AN: 4706

European-Finnish (FIN) AF: 0.00548 AC: 55 AN: 10036

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.0314 AC: 2100 AN: 66906

Other (OTH) AF: 0.0957 AC: 195 AN: 2038

Alfa AF: 0.0147 Hom.: 19

Bravo AF: 0.0966

Asia WGS AF: 0.0850 AC: 293 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.4
DANN	Benign	0.83
PhyloP100		0.78
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1266078; hg19: chr6-31622043;