6-31655116-T-C

Position:

• chr6-31655116-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOM	NM_001256169.2	c.-102-1356T>C		intron_variant			NP_001243098.1
APOM	NR_045828.2	n.149-1356T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOM	ENST00000375920.8	c.-102-1356T>C		intron_variant		1		ENSP00000365085
APOM	ENST00000375918.6	c.-102-1356T>C		intron_variant		2		ENSP00000365083

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

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0448

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0300

Gnomad4 FIN AF: 0.00424

Gnomad4 NFE AF: 0.0172

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.00442 Hom.: 1

Bravo AF: 0.0577

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs805296; hg19: chr6-31622893;