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rs16891982

chr5-33951588-C-Achr5-33951588-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM2_Supporting

The NM_016180(SLC45A2):c.1122G>T(p.Leu374Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 152080 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Benignin ClinVar.

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)

Consequence

SLC45A2
NM_016180 missense

Scores

4
12
3

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.55

Links

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, gnomad allele frequency = 0.0000132 (2/152080) while in subpopulation AFR AF= 0.0000242 (1/41362). AF 95% confidence interval is 0. There are 0 homozygotes in gnomad. There are 0 alleles in male gnomad subpopulation. Median coverage is 32. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC45A2NM_016180.5 linkuse as main transcriptc.1122G>T p.Leu374Phe missense_variant 5/7 ENST00000296589.9
SLC45A2NM_001012509.4 linkuse as main transcriptc.1122G>T p.Leu374Phe missense_variant 5/6
SLC45A2XM_047417259.1 linkuse as main transcriptc.882G>T p.Leu294Phe missense_variant 5/7
SLC45A2NM_001297417.4 linkuse as main transcriptc.*64G>T 3_prime_UTR_variant 4/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC45A2ENST00000296589.9 linkuse as main transcriptc.1122G>T p.Leu374Phe missense_variant 5/71 NM_016180.5 P1Q9UMX9-1
SLC45A2ENST00000382102.7 linkuse as main transcriptc.1122G>T p.Leu374Phe missense_variant 5/61 Q9UMX9-4
SLC45A2ENST00000509381.1 linkuse as main transcriptc.*64G>T 3_prime_UTR_variant 4/41
SLC45A2ENST00000510600.1 linkuse as main transcriptc.597G>T p.Leu199Phe missense_variant 4/53

Frequencies

GnomAD3 genomes
AF:
0.0000132
AC:
2
AN:
152080
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000242
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461858
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
727234
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.0000166
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.57
BayesDel_addAF
Pathogenic
0.19
D
BayesDel_noAF
Uncertain
0.040
Cadd
Uncertain
24
Dann
Uncertain
1.0
DEOGEN2
Uncertain
0.74
D;.;.
Eigen
Uncertain
0.58
Eigen_PC
Uncertain
0.52
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Benign
0.71
T;T;T
M_CAP
Uncertain
0.15
D
MetaRNN
Uncertain
0.71
D;D;D
MetaSVM
Uncertain
0.61
D
MutationAssessor
Pathogenic
3.0
M;M;.
MutationTaster
Benign
1.0
D;D;D;D;N
PrimateAI
Benign
0.39
T
PROVEAN
Uncertain
-2.7
D;D;D
REVEL
Pathogenic
0.70
Sift
Uncertain
0.0030
D;D;D
Sift4G
Uncertain
0.0050
D;D;D
Polyphen
0.99
D;D;.
Vest4
0.20
MutPred
0.50
Gain of helix (P = 0.2294);Gain of helix (P = 0.2294);.;
MVP
0.85
MPC
0.27
ClinPred
0.98
D
GERP RS
4.3
Varity_R
0.39
gMVP
0.90

Splicing

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: rs16891982; hg19: chr5-33951693;