6-31654829-C-A

Position:

• chr6-31654829-C-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
APOM	NM_001256169.2	c.-102-1643C>A		intron_variant			NP_001243098.1
APOM	NR_045828.2	n.149-1643C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOM	ENST00000375920.8	c.-102-1643C>A		intron_variant		1		ENSP00000365085
APOM	ENST00000375918.6	c.-102-1643C>A		intron_variant		2		ENSP00000365083

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

Gnomad4 AFR AF: 0.0537

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.267

Alfa AF: 0.316 Hom.: 12038

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs805297; hg19: chr6-31622606;