6-31655039-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000375920.8(APOM):c.-102-1433T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.048 in 152,262 control chromosomes in the GnomAD database, including 325 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.048 (325 hom., cov: 32)
• Consequence: APOM ENST00000375920.8 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0640

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 6-31655039-T-C is Benign according to our data. Variant chr6-31655039-T-C is described in ClinVar as [Benign]. Clinvar id is 2920838.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOM	NM_001256169.2	c.-102-1433T>C		intron_variant
APOM	NR_045828.2	n.149-1433T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOM	ENST00000375920.8	c.-102-1433T>C		intron_variant		1
APOM	ENST00000375918.6	c.-102-1433T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0480 AC: 7309 AN: 152144 Hom.: 325 Cov.: 32

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0323

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0570

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0480 AC: 7307 AN: 152262 Hom.: 325 Cov.: 32 AF XY: 0.0494 AC XY: 3680 AN XY: 74454

Gnomad4 AFR AF: 0.0103

Gnomad4 AMR AF: 0.0324

Gnomad4 ASJ AF: 0.0599

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0333

Gnomad4 NFE AF: 0.0570

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0478 Hom.: 26

Bravo AF: 0.0450

Asia WGS AF: 0.124 AC: 428 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Nov 02, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.3
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9404941; hg19: chr6-31622816;