rs779248044

Variant names:

• chr20-24970239-C-G
• rs779248044
• NM_020531.3:c.671G>C

Your query was ambiguous. Multiple possible variants found:

• chr20-24970239-C-G
• chr20-24970239-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_020531.3(APMAP):​c.671G>C​(p.Arg224Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic 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. R224Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: APMAP NM_020531.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.89
• Publications: 0 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 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.872

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.671G>C	p.Arg224Pro	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.671G>C	p.Arg224Pro	missense	Exon 6 of 9	ENSP00000217456.2	Q9HDC9-1
	APMAP	ENST00000932674.1		c.671G>C	p.Arg224Pro	missense	Exon 6 of 11	ENSP00000602733.1
	APMAP	ENST00000881539.1		c.671G>C	p.Arg224Pro	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

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.83
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Uncertain	0.11
CADD	Uncertain	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.077	T
Eigen	Uncertain	0.62
Eigen_PC	Uncertain	0.60
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.94	D
M_CAP	Benign	0.037	D
MetaRNN	Pathogenic	0.87	D
MetaSVM	Benign	-0.67	T
MutationAssessor	Benign	1.8	L
PhyloP100		3.9
PrimateAI	Benign	0.45	T
PROVEAN	Uncertain	-3.3	D
REVEL	Uncertain	0.37
Sift	Uncertain	0.0050	D
Sift4G	Benign	0.12	T
Polyphen		1.0	D
Vest4		0.81
MutPred		0.70		Loss of MoRF binding (P = 0.0286)
MVP		0.77
MPC		0.95
ClinPred		0.94	D
GERP RS		5.8
Varity_R		0.88
gMVP		0.85
Mutation Taster		=28/72	disease causing

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: rs779248044; hg19: chr20-24950875;