ENST00000375920.8:c.-102-1356T>C

Variant names:

• chr6-31655116-T-C
• rs805296
• ENST00000375920.8:c.-102-1356T>C

Variant summary

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

The ENST00000375920.8(APOM):​c.-102-1356T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0513 in 152,270 control chromosomes in the GnomAD database, including 356 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 0.051 (356 hom., cov: 32)
• Consequence: APOM ENST00000375920.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 35 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000375920.8. 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.-102-1356T>C		intron	N/A	NP_001243098.1	O95445-2
	APOM	NR_045828.2		n.149-1356T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOM	ENST00000375920.8	TSL:1	c.-102-1356T>C		intron	N/A	ENSP00000365085.4	O95445-2
	APOM	ENST00000375918.6	TSL:2	c.-102-1356T>C		intron	N/A	ENSP00000365083.2	Q5SRP5

Frequencies

GnomAD3 genomes AF: 0.0513 AC: 7800 AN: 152152 Hom.: 356 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0449

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0300

Gnomad FIN AF: 0.00424

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0513 AC: 7808 AN: 152270 Hom.: 356 Cov.: 32 AF XY: 0.0512 AC XY: 3816 AN XY: 74464

African (AFR) AF: 0.120 AC: 4998 AN: 41538

American (AMR) AF: 0.0448 AC: 685 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0248 AC: 86 AN: 3468

East Asian (EAS) AF: 0.109 AC: 566 AN: 5180

South Asian (SAS) AF: 0.0300 AC: 145 AN: 4826

European-Finnish (FIN) AF: 0.00424 AC: 45 AN: 10620

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0172 AC: 1173 AN: 68028

Other (OTH) AF: 0.0445 AC: 94 AN: 2112

Alfa AF: 0.00944 Hom.: 8

Bravo AF: 0.0577

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.84
PhyloP100		-1.9
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: rs805296; hg19: chr6-31622893;