rs2016586

Variant names:

• chr22-35729217-T-C
• rs2016586
• NM_030642.1:c.*7-137T>C

Your query was ambiguous. Multiple possible variants found:

• chr22-35729217-T-C
• chr22-35729217-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_030642.1(APOL5):​c.*7-137T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: APOL5 NM_030642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 7 publications found

Genes affected

APOL5 (HGNC:14869): (apolipoprotein L5) This gene is a member of the apolipoprotein L gene family. The encoded protein is found in the cytoplasm, where it may affect the movement of lipids or allow the binding of lipids to organelles. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOL5	NM_030642.1	c.*7-137T>C		intron_variant	Intron 4 of 4	ENST00000249044.2	NP_085145.1
APOL5	XM_006724321.5	c.*7-137T>C		intron_variant	Intron 5 of 5		XP_006724384.1
APOL5	XM_017028945.3	c.*7-137T>C		intron_variant	Intron 4 of 4		XP_016884434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOL5	ENST00000249044.2	c.*7-137T>C		intron_variant	Intron 4 of 4	1	NM_030642.1	ENSP00000249044.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 110610 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 55710

African (AFR) AF: 0.00 AC: 0 AN: 2990

American (AMR) AF: 0.00 AC: 0 AN: 2192

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4076

East Asian (EAS) AF: 0.00 AC: 0 AN: 5626

South Asian (SAS) AF: 0.00 AC: 0 AN: 7480

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6998

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 612

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 72968

Other (OTH) AF: 0.00 AC: 0 AN: 7668

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.78
PhyloP100		-0.36

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: rs2016586; hg19: chr22-36125264;