ENST00000543404.5:n.599G>C

Variant names:

• chr12-9232362-C-G
• rs16918212
• ENST00000543404.5:n.599G>C

Variant summary

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

The ENST00000543404.5(A2MP1):​n.599G>C variant causes a splice region, non coding transcript exon change. 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)
• Consequence: A2MP1 ENST00000543404.5 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.73
• Publications: 7 publications found

Genes affected

A2MP1 (HGNC:):

A2MP1 (HGNC:8): (alpha-2-macroglobulin pseudogene 1)

LINC00987 (HGNC:48911): (long intergenic non-protein coding RNA 987)

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 (BayesDel_noAF=-0.24).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000543404.5. 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
	A2MP1	NR_040112.1		n.599G>C		splice_region non_coding_transcript_exon	Exon 3 of 9
	A2MP1	NR_199634.1		n.3387G>C		splice_region non_coding_transcript_exon	Exon 24 of 30

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	A2MP1	ENST00000543404.5	TSL:5	n.599G>C		splice_region non_coding_transcript_exon	Exon 3 of 9
	A2MP1	ENST00000566278.6	TSL:6	n.3698G>C		splice_region non_coding_transcript_exon	Exon 27 of 32
	LINC00987	ENST00000838855.1		n.99-14107C>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	16
DANN	Benign	0.79
PhyloP100		5.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16918212;

hg19: chr12-9384958;