chr7-151086820-GC-G

Variant names:

• chr7-151086820-GC-G
• rs886043141
• NM_031946.7:c.80delC

Variant summary

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

The NM_031946.7(AGAP3):​c.80delC​(p.Ala27GlyfsTer63) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: AGAP3 NM_031946.7 frameshift
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.374
• Publications: 3 publications found

Genes affected

AGAP3 (HGNC:16923): (ArfGAP with GTPase domain, ankyrin repeat and PH domain 3) This gene encodes an essential component of the N-methyl-D-aspartate (NMDA) receptor signaling complex which mediates long-term potentiation in synapses by linking activation of NMDA receptor to alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor trafficking. The encoded protein contains an N-terminal GTPase-like domain, a pleckstrin homology domain, an ArfGAP domain and several C-terminal ankryn repeat domains. [provided by RefSeq, Apr 2017]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031946.7. 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
	AGAP3	NM_031946.7	MANE Select	c.80delC	p.Ala27GlyfsTer63	frameshift	Exon 1 of 18	NP_114152.3
	AGAP3	NM_001350102.2		c.80delC	p.Ala27GlyfsTer63	frameshift	Exon 1 of 16	NP_001337031.1
	AGAP3	NM_001042535.4		c.80delC	p.Ala27GlyfsTer63	frameshift	Exon 1 of 9	NP_001036000.1	Q96P47-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGAP3	ENST00000397238.7	TSL:1 MANE Select	c.80delC	p.Ala27GlyfsTer63	frameshift	Exon 1 of 18	ENSP00000380413.2	Q96P47-4
	AGAP3	ENST00000473312.5	TSL:1	c.80delC	p.Ala27GlyfsTer63	frameshift	Exon 1 of 9	ENSP00000418921.1	Q96P47-6
	AGAP3	ENST00000961568.1		c.80delC	p.Ala27GlyfsTer63	frameshift	Exon 1 of 19	ENSP00000631627.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 797850 Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0 AN XY: 368666

African (AFR) AF: 0.00 AC: 0 AN: 15086

American (AMR) AF: 0.00 AC: 0 AN: 944

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4940

East Asian (EAS) AF: 0.00 AC: 0 AN: 3446

South Asian (SAS) AF: 0.00 AC: 0 AN: 16562

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 264

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1576

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 728870

Other (OTH) AF: 0.00 AC: 0 AN: 26162

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.37

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: rs886043141; hg19: chr7-150783907;