rs368403887

Variant names:

• chr22-36227796-T-A
• NM_030882.4:c.622A>T

Your query was ambiguous. Multiple possible variants found:

• chr22-36227796-T-A
• chr22-36227796-T-C
• chr22-36227796-T-G

Variant summary

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

The NM_030882.4(APOL2):​c.622A>T​(p.Thr208Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T208I) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: APOL2 NM_030882.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

Genes affected

APOL2 (HGNC:619): (apolipoprotein L2) 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. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

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 (MetaRNN=0.030838192).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOL2	NM_030882.4	c.622A>T	p.Thr208Ser	missense_variant	Exon 5 of 5	ENST00000358502.10	NP_112092.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOL2	ENST00000358502.10	c.622A>T	p.Thr208Ser	missense_variant	Exon 5 of 5	1	NM_030882.4	ENSP00000351292.5
APOL2	ENST00000249066.10	c.622A>T	p.Thr208Ser	missense_variant	Exon 6 of 6	1		ENSP00000249066.6
APOL2	ENST00000451256.6	c.958A>T	p.Thr320Ser	missense_variant	Exon 6 of 6	2		ENSP00000403153.2
APOL2	ENST00000529194.5	c.*236A>T		downstream_gene_variant		3		ENSP00000431231.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461884 Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1 AN XY: 727244

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: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.082
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.0030
DANN	Benign	0.10
DEOGEN2	Benign	0.0052	.;.;T
Eigen	Benign	-2.1
Eigen_PC	Benign	-2.1
FATHMM_MKL	Benign	0.00039	N
LIST_S2	Benign	0.23	.;T;T
M_CAP	Benign	0.0035	T
MetaRNN	Benign	0.031	T;T;T
MetaSVM	Benign	-0.96	T
PrimateAI	Benign	0.31	T
PROVEAN	Benign	1.6	N;N;N
REVEL	Benign	0.019
Sift	Benign	1.0	T;T;T
Sift4G	Benign	1.0	T;T;T
Vest4		0.011
MutPred		0.49		Gain of MoRF binding (P = 0.1211);Gain of MoRF binding (P = 0.1211);.;
MVP		0.17
MPC		0.062
ClinPred		0.052	T
GERP RS		-3.7
gMVP		0.078

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: chr22-36623842;