rs17473271

chr10-69089146-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002727.4(SRGN):c.79+910G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,090 control chromosomes in the GnomAD database, including 3,307 homozygotes. 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: 𝑓 0.19 (3307 hom., cov: 32)
• Consequence: SRGN NM_002727.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRGN	NM_002727.4	c.79+910G>A		intron_variant		ENST00000242465.4
SRGN	NM_001321053.2	c.79+910G>A		intron_variant
SRGN	NM_001321054.1	c.59+910G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRGN	ENST00000242465.4	c.79+910G>A		intron_variant		1	NM_002727.4	P1
SRGN	ENST00000462445.1	n.131+910G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28568 AN: 151972 Hom.: 3301 Cov.: 32

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.188 AC: 28594 AN: 152090 Hom.: 3307 Cov.: 32 AF XY: 0.191 AC XY: 14170 AN XY: 74336

Gnomad4 AFR AF: 0.0869

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.172

Alfa AF: 0.197 Hom.: 480

Bravo AF: 0.167

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	1.6
Dann	Benign	0.84

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

Publications

LitVar

Other links and lift over

dbSNP: rs17473271; hg19: chr10-70848902;