rs34490746

Variant names:

• chr6-31657231-T-C
• rs34490746
• NM_019101.3:c.276T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-31657231-T-C
• chr6-31657231-T-G

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Strong BP7 BS2

The NM_019101.3(APOM):​c.276T>C​(p.Asp92Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00055 in 1,612,836 control chromosomes in the GnomAD database, including 11 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 0.0029 (6 hom., cov: 31)
  • Exomes 𝑓: 0.00030 (5 hom.)
• Consequence: APOM NM_019101.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 2 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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BP7: Synonymous conserved (PhyloP=-0.224 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 6 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019101.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOM	NM_019101.3	MANE Select	c.276T>C	p.Asp92Asp	synonymous	Exon 3 of 6	NP_061974.2
	APOM	NM_001256169.2		c.60T>C	p.Asp20Asp	synonymous	Exon 3 of 6	NP_001243098.1	O95445-2
	APOM	NR_045828.2		n.317T>C		non_coding_transcript_exon	Exon 3 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOM	ENST00000375916.4	TSL:1 MANE Select	c.276T>C	p.Asp92Asp	synonymous	Exon 3 of 6	ENSP00000365081.3	O95445-1
	APOM	ENST00000375920.8	TSL:1	c.60T>C	p.Asp20Asp	synonymous	Exon 3 of 6	ENSP00000365085.4	O95445-2
	APOM	ENST00000375918.6	TSL:2	c.60T>C	p.Asp20Asp	synonymous	Exon 3 of 5	ENSP00000365083.2	Q5SRP5

Frequencies

GnomAD3 genomes AF: 0.00290 AC: 441 AN: 151990 Hom.: 6 Cov.: 31

Gnomad AFR AF: 0.00996

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00151

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.000960

GnomAD2 exomes AF: 0.000649 AC: 160 AN: 246620 AF XY: 0.000394

Gnomad AFR exome AF: 0.00801

Gnomad AMR exome AF: 0.000986

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000271

Gnomad OTH exome AF: 0.000329

GnomAD4 exome AF: 0.000304 AC: 444 AN: 1460754 Hom.: 5 Cov.: 32 AF XY: 0.000231 AC XY: 168 AN XY: 726690

African (AFR) AF: 0.00959 AC: 321 AN: 33478

American (AMR) AF: 0.00105 AC: 47 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.0000348 AC: 3 AN: 86256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52316

Middle Eastern (MID) AF: 0.000173 AC: 1 AN: 5768

European-Non Finnish (NFE) AF: 0.0000189 AC: 21 AN: 1111992

Other (OTH) AF: 0.000845 AC: 51 AN: 60384

GnomAD4 genome AF: 0.00291 AC: 443 AN: 152082 Hom.: 6 Cov.: 31 AF XY: 0.00276 AC XY: 205 AN XY: 74334

African (AFR) AF: 0.00999 AC: 414 AN: 41462

American (AMR) AF: 0.00151 AC: 23 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10560

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 68008

Other (OTH) AF: 0.000951 AC: 2 AN: 2102

Alfa AF: 0.000778 Hom.: 1

Bravo AF: 0.00340

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.000164

EpiControl AF: 0.000119

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	4.8
DANN	Benign	0.64
PhyloP100		-0.22
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs34490746; hg19: chr6-31625008;