1-153003830-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000295367.5(SPRR3):​c.*300T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 438,488 control chromosomes in the GnomAD database, including 64,140 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 0.53 ( 21531 hom., cov: 32)
Exomes 𝑓: 0.54 ( 42609 hom. )

Consequence

SPRR3
ENST00000295367.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.00
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SPRR3NM_001097589.2 linkuse as main transcriptc.*300T>G 3_prime_UTR_variant 2/2 ENST00000295367.5 NP_001091058.1
SPRR3NM_005416.3 linkuse as main transcriptc.*300T>G 3_prime_UTR_variant 3/3 NP_005407.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SPRR3ENST00000295367.5 linkuse as main transcriptc.*300T>G 3_prime_UTR_variant 2/21 NM_001097589.2 ENSP00000295367 P1
SPRR3ENST00000331860.7 linkuse as main transcriptc.*300T>G 3_prime_UTR_variant 3/33 ENSP00000330391 P1

Frequencies

GnomAD3 genomes
AF:
0.530
AC:
80565
AN:
151900
Hom.:
21505
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.515
Gnomad AMI
AF:
0.438
Gnomad AMR
AF:
0.484
Gnomad ASJ
AF:
0.570
Gnomad EAS
AF:
0.653
Gnomad SAS
AF:
0.523
Gnomad FIN
AF:
0.509
Gnomad MID
AF:
0.513
Gnomad NFE
AF:
0.544
Gnomad OTH
AF:
0.527
GnomAD4 exome
AF:
0.539
AC:
154537
AN:
286470
Hom.:
42609
Cov.:
3
AF XY:
0.540
AC XY:
80085
AN XY:
148392
show subpopulations
Gnomad4 AFR exome
AF:
0.515
Gnomad4 AMR exome
AF:
0.469
Gnomad4 ASJ exome
AF:
0.568
Gnomad4 EAS exome
AF:
0.659
Gnomad4 SAS exome
AF:
0.519
Gnomad4 FIN exome
AF:
0.513
Gnomad4 NFE exome
AF:
0.540
Gnomad4 OTH exome
AF:
0.530
GnomAD4 genome
AF:
0.530
AC:
80643
AN:
152018
Hom.:
21531
Cov.:
32
AF XY:
0.527
AC XY:
39181
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.515
Gnomad4 AMR
AF:
0.484
Gnomad4 ASJ
AF:
0.570
Gnomad4 EAS
AF:
0.653
Gnomad4 SAS
AF:
0.523
Gnomad4 FIN
AF:
0.509
Gnomad4 NFE
AF:
0.544
Gnomad4 OTH
AF:
0.527
Alfa
AF:
0.536
Hom.:
6637
Bravo
AF:
0.530
Asia WGS
AF:
0.547
AC:
1903
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
2.1
DANN
Benign
0.82

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1134220; hg19: chr1-152976306; API