rs895578255

Variant names:

• chr20-24970345-C-G
• rs895578255
• NM_020531.3:c.565G>C

Your query was ambiguous. Multiple possible variants found:

• chr20-24970345-C-G
• chr20-24970345-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020531.3(APMAP):​c.565G>C​(p.Glu189Gln) variant causes a missense 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. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E189K) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: APMAP NM_020531.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.00
• Publications: 1 publications found

Genes affected

APMAP (HGNC:13238): (adipocyte plasma membrane associated protein) Enables arylesterase activity. Predicted to be involved in biosynthetic process. Located in cell surface and membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06824991).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020531.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APMAP	NM_020531.3	MANE Select	c.565G>C	p.Glu189Gln	missense	Exon 6 of 9	NP_065392.1	Q9HDC9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APMAP	ENST00000217456.3	TSL:1 MANE Select	c.565G>C	p.Glu189Gln	missense	Exon 6 of 9	ENSP00000217456.2	Q9HDC9-1
	APMAP	ENST00000932674.1		c.565G>C	p.Glu189Gln	missense	Exon 6 of 11	ENSP00000602733.1
	APMAP	ENST00000881539.1		c.565G>C	p.Glu189Gln	missense	Exon 6 of 10	ENSP00000551598.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.079
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	17
DANN	Benign	0.97
DEOGEN2	Benign	0.0031	T
Eigen	Benign	-0.43
Eigen_PC	Benign	-0.28
FATHMM_MKL	Benign	0.63	D
LIST_S2	Benign	0.78	T
M_CAP	Benign	0.0044	T
MetaRNN	Benign	0.068	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.78	N
PhyloP100		1.0
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-0.24	N
REVEL	Benign	0.058
Sift	Benign	0.37	T
Sift4G	Benign	0.61	T
Polyphen		0.0	B
Vest4		0.062
MutPred		0.53		Loss of disorder (P = 0.1017)
MVP		0.46
MPC		0.21
ClinPred		0.13	T
GERP RS		3.3
Varity_R		0.063
gMVP		0.55
Mutation Taster		=90/10	polymorphism

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: rs895578255; hg19: chr20-24950981;