NM_001638.4:c.16+118T>G

Variant names:

• chr12-56362612-A-C
• rs78739461
• NM_001638.4:c.16+118T>G

Variant summary

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

The NM_001638.4(APOF):​c.16+118T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00898 in 1,011,424 control chromosomes in the GnomAD database, including 61 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 0.0079 (9 hom., cov: 32)
  • Exomes 𝑓: 0.0092 (52 hom.)
• Consequence: APOF NM_001638.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

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=-0.74).
• BS1: Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00917 (7879/859336) while in subpopulation MID AF= 0.0196 (71/3630). AF 95% confidence interval is 0.0159. There are 52 homozygotes in gnomad4_exome. There are 4119 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOF	NM_001638.4	c.16+118T>G		intron_variant	Intron 1 of 1	ENST00000398189.4	NP_001629.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOF	ENST00000398189.4	c.16+118T>G		intron_variant	Intron 1 of 1	1	NM_001638.4	ENSP00000381250.3

Frequencies

GnomAD3 genomes AF: 0.00789 AC: 1199 AN: 151970 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.00160

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.00964

Gnomad ASJ AF: 0.0563

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00643

Gnomad FIN AF: 0.00425

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00987

Gnomad OTH AF: 0.0125

GnomAD4 exome AF: 0.00917 AC: 7879 AN: 859336 Hom.: 52 AF XY: 0.00937 AC XY: 4119 AN XY: 439422

Gnomad4 AFR exome AF: 0.00225

Gnomad4 AMR exome AF: 0.00871

Gnomad4 ASJ exome AF: 0.0454

Gnomad4 EAS exome AF: 0.0000878

Gnomad4 SAS exome AF: 0.00645

Gnomad4 FIN exome AF: 0.00519

Gnomad4 NFE exome AF: 0.00909

Gnomad4 OTH exome AF: 0.0126

GnomAD4 genome AF: 0.00788 AC: 1199 AN: 152088 Hom.: 9 Cov.: 32 AF XY: 0.00742 AC XY: 552 AN XY: 74352

Gnomad4 AFR AF: 0.00159

Gnomad4 AMR AF: 0.00963

Gnomad4 ASJ AF: 0.0563

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00644

Gnomad4 FIN AF: 0.00425

Gnomad4 NFE AF: 0.00989

Gnomad4 OTH AF: 0.0123

Alfa AF: 0.00823 Hom.: 1

Bravo AF: 0.00830

Asia WGS AF: 0.00289 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs78739461; hg19: chr12-56756396;