22-36204690-A-T

Variant names:

• chr22-36204690-A-T
• ENST00000352371.5:c.-82T>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_145660.2(APOL4):​c.-82T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000069 in 434,666 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0000069 (0 hom.)
• Consequence: APOL4 NM_145660.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

Genes affected

APOL4 (HGNC:14867): (apolipoprotein L4) This gene encodes a member of the apolipoprotein L family. The encoded protein may play a role in lipid exchange and transport throughout the body, as well as in reverse cholesterol transport from peripheral cells to the liver. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2020]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOL4	NM_145660.2	c.-82T>A		5_prime_UTR_variant	Exon 1 of 5		NP_663693.1
APOL4	NM_030643.4	c.-280T>A		5_prime_UTR_variant	Exon 1 of 6		NP_085146.2
APOL4	NM_145661.2	c.-280T>A		5_prime_UTR_variant	Exon 1 of 6		NP_663694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOL4	ENST00000352371.5	c.-82T>A		5_prime_UTR_variant	Exon 1 of 5	1		ENSP00000338260.3
APOL4	ENST00000616056.4	c.-280T>A		5_prime_UTR_variant	Exon 1 of 6	1		ENSP00000483497.1
APOL4	ENST00000397275.6	c.-280T>A		5_prime_UTR_variant	Exon 1 of 6	1		ENSP00000380445.2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000690 AC: 3 AN: 434666 Hom.: 0 Cov.: 6 AF XY: 0.00000875 AC XY: 2 AN XY: 228520

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000979

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.52

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-36600736;