rs805297

Variant names:

• chr6-31654829-C-A
• rs805297
• ENST00000375920.8:c.-102-1643C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31654829-C-A
• chr6-31654829-C-G
• chr6-31654829-C-T

Variant summary

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

The ENST00000375920.8(APOM):​c.-102-1643C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,132 control chromosomes in the GnomAD database, including 5,590 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 0.24 (5590 hom., cov: 32)
• Consequence: APOM ENST00000375920.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 88 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOM	NM_001256169.2	c.-102-1643C>A		intron_variant	Intron 1 of 5		NP_001243098.1
APOM	NR_045828.2	n.149-1643C>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOM	ENST00000375920.8	c.-102-1643C>A		intron_variant	Intron 1 of 5	1		ENSP00000365085.4
APOM	ENST00000375918.6	c.-102-1643C>A		intron_variant	Intron 1 of 4	2		ENSP00000365083.2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36575 AN: 152014 Hom.: 5589 Cov.: 32

Gnomad AFR AF: 0.0538

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.240 AC: 36579 AN: 152132 Hom.: 5590 Cov.: 32 AF XY: 0.243 AC XY: 18106 AN XY: 74366

African (AFR) AF: 0.0537 AC: 2230 AN: 41522

American (AMR) AF: 0.302 AC: 4616 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1689 AN: 3468

East Asian (EAS) AF: 0.361 AC: 1872 AN: 5184

South Asian (SAS) AF: 0.314 AC: 1519 AN: 4830

European-Finnish (FIN) AF: 0.282 AC: 2982 AN: 10558

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20680 AN: 67972

Other (OTH) AF: 0.267 AC: 564 AN: 2116

Alfa AF: 0.295 Hom.: 28456

Bravo AF: 0.234

Asia WGS AF: 0.299 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.4
DANN	Benign	0.81
PhyloP100		-1.6
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: rs805297; hg19: chr6-31622606;