1-153003239-C-T

Variant names:

• chr1-153003239-C-T
• rs28989168
• NM_001097589.2:c.219C>T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_001097589.2(SPRR3):​c.219C>T​(p.Gly73Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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 0.0015 (0 hom., cov: 0)
  • Exomes 𝑓: 0.027 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPRR3 NM_001097589.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

Genes affected

SPRR3 (HGNC:11268): (small proline rich protein 3) Predicted to enable structural molecule activity. Predicted to be involved in wound healing. Located in Golgi apparatus and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP7: Synonymous conserved (PhyloP=-0.147 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPRR3	NM_001097589.2	c.219C>T	p.Gly73Gly	synonymous_variant	Exon 2 of 2	ENST00000295367.5	NP_001091058.1
SPRR3	NM_005416.3	c.219C>T	p.Gly73Gly	synonymous_variant	Exon 3 of 3		NP_005407.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPRR3	ENST00000295367.5	c.219C>T	p.Gly73Gly	synonymous_variant	Exon 2 of 2	1	NM_001097589.2	ENSP00000295367.4
SPRR3	ENST00000331860.7	c.219C>T	p.Gly73Gly	synonymous_variant	Exon 3 of 3	3		ENSP00000330391.3
SPRR3	ENST00000443178.1	c.219C>T	p.Gly73Gly	synonymous_variant	Exon 3 of 3	3		ENSP00000402016.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 46 AN: 30528 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00617

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000753

Gnomad ASJ AF: 0.00130

Gnomad EAS AF: 0.00542

Gnomad SAS AF: 0.00412

Gnomad FIN AF: 0.000360

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000316

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000633 AC: 112 AN: 176836 Hom.: 0 AF XY: 0.000696 AC XY: 67 AN XY: 96324

Gnomad AFR exome AF: 0.0000983

Gnomad AMR exome AF: 0.000169

Gnomad ASJ exome AF: 0.00144

Gnomad EAS exome AF: 0.0000977

Gnomad SAS exome AF: 0.00116

Gnomad FIN exome AF: 0.000409

Gnomad NFE exome AF: 0.000749

Gnomad OTH exome AF: 0.000516

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0274 AC: 20489 AN: 747626 Hom.: 1 Cov.: 30 AF XY: 0.0258 AC XY: 9960 AN XY: 385366

Gnomad4 AFR exome AF: 0.0443

Gnomad4 AMR exome AF: 0.00280

Gnomad4 ASJ exome AF: 0.0164

Gnomad4 EAS exome AF: 0.00371

Gnomad4 SAS exome AF: 0.0116

Gnomad4 FIN exome AF: 0.00156

Gnomad4 NFE exome AF: 0.0347

Gnomad4 OTH exome AF: 0.0210

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00151 AC: 46 AN: 30524 Hom.: 0 Cov.: 0 AF XY: 0.00185 AC XY: 28 AN XY: 15144

Gnomad4 AFR AF: 0.00617

Gnomad4 AMR AF: 0.000752

Gnomad4 ASJ AF: 0.00130

Gnomad4 EAS AF: 0.00542

Gnomad4 SAS AF: 0.00413

Gnomad4 FIN AF: 0.000360

Gnomad4 NFE AF: 0.000315

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000776 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.29

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: rs28989168; hg19: chr1-152975715; COSMIC: COSV54878285; COSMIC: COSV54878285;