chr12-56362392-C-T

Position:

• chr12-56362392-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001638.4(APOF):​c.17-203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0174 in 152,190 control chromosomes in the GnomAD database, including 36 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 0.017 (36 hom., cov: 32)
• Consequence: APOF NM_001638.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

APOF (HGNC:615): (apolipoprotein F) The product of this gene is one of the minor apolipoproteins found in plasma. This protein forms complexes with lipoproteins and may be involved in transport and/or esterification of cholesterol. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0174 (2652/152190) while in subpopulation NFE AF= 0.0303 (2062/68016). AF 95% confidence interval is 0.0292. There are 36 homozygotes in gnomad4. There are 1209 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 36 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOF	NM_001638.4	c.17-203G>A		intron_variant		ENST00000398189.4	NP_001629.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOF	ENST00000398189.4	c.17-203G>A		intron_variant		1	NM_001638.4	ENSP00000381250.3

Frequencies

GnomAD3 genomes AF: 0.0174 AC: 2652 AN: 152072 Hom.: 36 Cov.: 32

Gnomad AFR AF: 0.00456

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0105

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00187

Gnomad FIN AF: 0.0142

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0303

Gnomad OTH AF: 0.0134

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

GnomAD4 genome AF: 0.0174 AC: 2652 AN: 152190 Hom.: 36 Cov.: 32 AF XY: 0.0162 AC XY: 1209 AN XY: 74406

Gnomad4 AFR AF: 0.00455

Gnomad4 AMR AF: 0.0105

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00187

Gnomad4 FIN AF: 0.0142

Gnomad4 NFE AF: 0.0303

Gnomad4 OTH AF: 0.0133

Alfa AF: 0.00913 Hom.: 1

Bravo AF: 0.0167

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs34934555; hg19: chr12-56756176;