NM_020531.3:c.*282A>G

Variant names:

• chr20-24963531-T-C
• rs5839
• NM_020531.3:c.*282A>G

Variant summary

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

The NM_020531.3(APMAP):​c.*282A>G variant causes a 3 prime UTR 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: APMAP NM_020531.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 4 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: 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=-0.89).

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.*282A>G		3_prime_UTR	Exon 9 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.*282A>G		3_prime_UTR	Exon 9 of 9	ENSP00000217456.2	Q9HDC9-1
	APMAP	ENST00000932674.1		c.*282A>G		3_prime_UTR	Exon 11 of 11	ENSP00000602733.1
	APMAP	ENST00000881539.1		c.*282A>G		3_prime_UTR	Exon 10 of 10	ENSP00000551598.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 293166 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 154006

African (AFR) AF: 0.00 AC: 0 AN: 8978

American (AMR) AF: 0.00 AC: 0 AN: 10734

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9150

East Asian (EAS) AF: 0.00 AC: 0 AN: 17708

South Asian (SAS) AF: 0.00 AC: 0 AN: 36076

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16430

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1264

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 175678

Other (OTH) AF: 0.00 AC: 0 AN: 17148

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.97
DANN	Benign	0.72
PhyloP100		-0.50
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs5839; hg19: chr20-24944167;