chr6-31654364-C-T

Position:

• chr6-31654364-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000375920.8(APOM):​c.-103+1813C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00582 in 152,194 control chromosomes in the GnomAD database, including 8 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 0.0058 (8 hom., cov: 32)
• Consequence: APOM ENST00000375920.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BS2: High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOM	NM_001256169.2	c.-103+1813C>T		intron_variant
APOM	NR_045828.2	n.148+1813C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOM	ENST00000375920.8	c.-103+1813C>T		intron_variant		1
APOM	ENST00000375918.6	c.-103+1813C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.00582 AC: 885 AN: 152076 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.00106

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.00694

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00768

Gnomad OTH AF: 0.00527

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

GnomAD4 genome AF: 0.00582 AC: 886 AN: 152194 Hom.: 8 Cov.: 32 AF XY: 0.00586 AC XY: 436 AN XY: 74424

Gnomad4 AFR AF: 0.00106

Gnomad4 AMR AF: 0.00693

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.00186

Gnomad4 FIN AF: 0.0113

Gnomad4 NFE AF: 0.00768

Gnomad4 OTH AF: 0.00521

Alfa AF: 0.00727 Hom.: 19

Bravo AF: 0.00544

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9267528; hg19: chr6-31622141;