chr1-153003830-T-C

Variant names:

• chr1-153003830-T-C
• rs1134220
• NM_001097589.2:c.*300T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001097589.2(SPRR3):​c.*300T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000348 in 287,360 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000035 (0 hom.)
• Consequence: SPRR3 NM_001097589.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 5 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001097589.2. 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
	SPRR3	NM_001097589.2	MANE Select	c.*300T>C		3_prime_UTR	Exon 2 of 2	NP_001091058.1
	SPRR3	NM_005416.3		c.*300T>C		3_prime_UTR	Exon 3 of 3	NP_005407.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPRR3	ENST00000295367.5	TSL:1 MANE Select	c.*300T>C		3_prime_UTR	Exon 2 of 2	ENSP00000295367.4
	SPRR3	ENST00000331860.7	TSL:3	c.*300T>C		3_prime_UTR	Exon 3 of 3	ENSP00000330391.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000348 AC: 1 AN: 287360 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 148846

African (AFR) AF: 0.00 AC: 0 AN: 9124

American (AMR) AF: 0.00 AC: 0 AN: 10586

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8842

East Asian (EAS) AF: 0.00 AC: 0 AN: 18132

South Asian (SAS) AF: 0.00 AC: 0 AN: 25118

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29202

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1230

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 168832

Other (OTH) AF: 0.0000614 AC: 1 AN: 16294

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.3
DANN	Benign	0.83
PhyloP100		-2.0

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: rs1134220; hg19: chr1-152976306;