10-69097096-GG-AA

Variant names:

• chr10-69097096-GG-AA
• NM_002727.4:c.92_93delGGinsAA
• SRGN p.Arg31Gln

Variant summary

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

The NM_002727.4(SRGN):​c.92_93delGGinsAA​(p.Arg31Gln) 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.

• Frequency: Genomes: not found (cov: 31)
• Consequence: SRGN NM_002727.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03
• Publications: 0 publications found

Genes affected

SRGN (HGNC:9361): (serglycin) This gene encodes a protein best known as a hematopoietic cell granule proteoglycan. Proteoglycans stored in the secretory granules of many hematopoietic cells also contain a protease-resistant peptide core, which may be important for neutralizing hydrolytic enzymes. This encoded protein was found to be associated with the macromolecular complex of granzymes and perforin, which may serve as a mediator of granule-mediated apoptosis. Two transcript variants, only one of them protein-coding, have been found for this gene. [provided by RefSeq, Jul 2010]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002727.4. 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
	SRGN	NM_002727.4	MANE Select	c.92_93delGGinsAA	p.Arg31Gln	missense	N/A	NP_002718.2
	SRGN	NM_001321053.2		c.92_93delGGinsAA	p.Arg31Gln	missense	N/A	NP_001307982.1	P10124
	SRGN	NM_001321054.1		c.60-6775_60-6774delGGinsAA		intron	N/A	NP_001307983.1	P10124

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRGN	ENST00000242465.4	TSL:1 MANE Select	c.92_93delGGinsAA	p.Arg31Gln	missense	N/A	ENSP00000242465.3	P10124
	SRGN	ENST00000718456.1		c.92_93delGGinsAA	p.Arg31Gln	missense	N/A	ENSP00000520834.1	P10124
	SRGN	ENST00000462445.1	TSL:2	n.132-6775_132-6774delGGinsAA		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.0

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: chr10-70856852;