16-57566656-GGG-CGA

Variant names:

• chr16-57566656-GGG-CGA
• NM_001304376.3:c.604_606delGGGinsCGA
• ADGRG5 p.Gly202Arg

Variant summary

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

The NM_001304376.3(ADGRG5):​c.604_606delGGGinsCGA​(p.Gly202Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G202W) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ADGRG5 NM_001304376.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.20
• Publications: 0 publications found

Genes affected

ADGRG5 (HGNC:19010): (adhesion G protein-coupled receptor G5) This gene encodes a member of the adhesion family of G-protein coupled receptors. Members of this family are characterized by long N-termini and multiple functional domains. They may play a role in the immune system as well as in the central nervous system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

LOC105371291 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304376.3. 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
	ADGRG5	NM_001304376.3	MANE Select	c.604_606delGGGinsCGA	p.Gly202Arg	missense	N/A	NP_001291305.1	Q8IZF4
	ADGRG5	NM_153837.4		c.604_606delGGGinsCGA	p.Gly202Arg	missense	N/A	NP_722579.1	Q8IZF4
	ADGRG5	NM_001318481.2		c.604_606delGGGinsCGA	p.Gly202Arg	missense	N/A	NP_001305410.1	B4E148

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRG5	ENST00000349457.8	TSL:1 MANE Select	c.604_606delGGGinsCGA	p.Gly202Arg	missense	N/A	ENSP00000290823.4	Q8IZF4
	ADGRG5	ENST00000340339.4	TSL:1	c.604_606delGGGinsCGA	p.Gly202Arg	missense	N/A	ENSP00000342981.4	Q8IZF4
	ADGRG5	ENST00000897109.1		c.604_606delGGGinsCGA	p.Gly202Arg	missense	N/A	ENSP00000567168.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.2

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

hg19: chr16-57600568;