Genetic Variant SPRR3:c.*300T>C (chr1-153003830-T-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.00

Publications

5 publications found

Variant links:

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]

SPRR3 links:

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ACMG classification

Classification was made for transcript

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPRR3	NM_001097589.2 link	c.*300T>C		3_prime_UTR_variant	Exon 2 of 2	ENST00000295367.5	NP_001091058.1	Q9UBC9
SPRR3	NM_005416.3 link	c.*300T>C		3_prime_UTR_variant	Exon 3 of 3		NP_005407.1	Q9UBC9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPRR3	ENST00000295367.5 link	c.*300T>C		3_prime_UTR_variant	Exon 2 of 2	1	NM_001097589.2	ENSP00000295367.4		Q9UBC9
SPRR3	ENST00000331860.7 link	c.*300T>C		3_prime_UTR_variant	Exon 3 of 3	3		ENSP00000330391.3		Q9UBC9

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000348

AC:

AN:

287360

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

148846

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

9124

American (AMR)

AF:

0.00

AC:

AN:

10586

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8842

East Asian (EAS)

AF:

0.00

AC:

AN:

18132

South Asian (SAS)

AF:

0.00

AC:

AN:

25118

European-Finnish (FIN)

AF:

0.00

AC:

AN:

29202

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1230

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

168832

Other (OTH)

AF:

0.0000614

AC:

AN:

16294

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

2.3

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over