6-31656096-G-A

Variant names:

• chr6-31656096-G-A
• rs805264
• NM_019101.3:c.114+16G>A

Variant summary

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

The NM_019101.3(APOM):​c.114+16G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0399 in 1,547,002 control chromosomes in the GnomAD database, including 2,040 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 0.066 (507 hom., cov: 32)
  • Exomes 𝑓: 0.037 (1533 hom.)
• Consequence: APOM NM_019101.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 18 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=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019101.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOM	NM_019101.3	MANE Select	c.114+16G>A		intron	N/A	NP_061974.2
	APOM	NM_001256169.2		c.-102-376G>A		intron	N/A	NP_001243098.1
	APOM	NR_045828.2		n.149-376G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOM	ENST00000375916.4	TSL:1 MANE Select	c.114+16G>A		intron	N/A	ENSP00000365081.3
	APOM	ENST00000375920.8	TSL:1	c.-102-376G>A		intron	N/A	ENSP00000365085.4
	APOM	ENST00000375918.6	TSL:2	c.-102-376G>A		intron	N/A	ENSP00000365083.2

Frequencies

GnomAD3 genomes AF: 0.0660 AC: 10048 AN: 152140 Hom.: 507 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0615

Gnomad ASJ AF: 0.0502

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0599

Gnomad FIN AF: 0.00584

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0289

Gnomad OTH AF: 0.0728

GnomAD2 exomes AF: 0.0508 AC: 8002 AN: 157474 AF XY: 0.0501

Gnomad AFR exome AF: 0.144

Gnomad AMR exome AF: 0.0531

Gnomad ASJ exome AF: 0.0498

Gnomad EAS exome AF: 0.144

Gnomad FIN exome AF: 0.00448

Gnomad NFE exome AF: 0.0293

Gnomad OTH exome AF: 0.0543

GnomAD4 exome AF: 0.0371 AC: 51742 AN: 1394744 Hom.: 1533 Cov.: 28 AF XY: 0.0372 AC XY: 25633 AN XY: 688832

African (AFR) AF: 0.145 AC: 4614 AN: 31778

American (AMR) AF: 0.0550 AC: 1979 AN: 35970

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 1303 AN: 25256

East Asian (EAS) AF: 0.0932 AC: 3381 AN: 36278

South Asian (SAS) AF: 0.0542 AC: 4306 AN: 79392

European-Finnish (FIN) AF: 0.00615 AC: 299 AN: 48604

Middle Eastern (MID) AF: 0.121 AC: 647 AN: 5350

European-Non Finnish (NFE) AF: 0.0300 AC: 32190 AN: 1074106

Other (OTH) AF: 0.0521 AC: 3023 AN: 58010

GnomAD4 genome AF: 0.0660 AC: 10052 AN: 152258 Hom.: 507 Cov.: 32 AF XY: 0.0660 AC XY: 4916 AN XY: 74442

African (AFR) AF: 0.139 AC: 5749 AN: 41508

American (AMR) AF: 0.0614 AC: 940 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0502 AC: 174 AN: 3466

East Asian (EAS) AF: 0.130 AC: 675 AN: 5182

South Asian (SAS) AF: 0.0598 AC: 289 AN: 4834

European-Finnish (FIN) AF: 0.00584 AC: 62 AN: 10622

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0289 AC: 1964 AN: 68032

Other (OTH) AF: 0.0725 AC: 153 AN: 2110

Alfa AF: 0.0436 Hom.: 964

Bravo AF: 0.0736

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.78
PhyloP100		0.19
PromoterAI		-0.016	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs805264; hg19: chr6-31623873; COSMIC: COSV52990956; COSMIC: COSV52990956;