10-13328315-C-T

Variant summary

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

The NM_012247.5(SEPHS1):​c.751+36G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,380,884 control chromosomes in the GnomAD database, including 190,224 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 0.45 ( 17097 hom., cov: 31)
Exomes 𝑓: 0.52 ( 173127 hom. )

Consequence

SEPHS1
NM_012247.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.733
Variant links:
Genes affected
SEPHS1 (HGNC:19685): (selenophosphate synthetase 1) This gene encodes an enzyme that synthesizes selenophosphate from selenide and ATP. Selenophosphate is the selenium donor used to synthesize selenocysteine, which is co-translationally incorporated into selenoproteins at in-frame UGA codons. [provided by RefSeq, Sep 2010]

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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SEPHS1NM_012247.5 linkc.751+36G>A intron_variant Intron 7 of 8 ENST00000327347.10 NP_036379.2 P49903-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SEPHS1ENST00000327347.10 linkc.751+36G>A intron_variant Intron 7 of 8 1 NM_012247.5 ENSP00000367893.3 P49903-1
SEPHS1ENST00000545675.5 linkc.550+36G>A intron_variant Intron 6 of 7 1 ENSP00000441119.2 P49903-3
SEPHS1ENST00000378614.8 linkc.751+36G>A intron_variant Intron 7 of 7 1 ENSP00000367877.3 P49903-2

Frequencies

GnomAD3 genomes
AF:
0.447
AC:
67826
AN:
151758
Hom.:
17099
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.206
Gnomad AMI
AF:
0.404
Gnomad AMR
AF:
0.599
Gnomad ASJ
AF:
0.455
Gnomad EAS
AF:
0.774
Gnomad SAS
AF:
0.598
Gnomad FIN
AF:
0.523
Gnomad MID
AF:
0.433
Gnomad NFE
AF:
0.511
Gnomad OTH
AF:
0.488
GnomAD3 exomes
AF:
0.544
AC:
132352
AN:
243390
Hom.:
38302
AF XY:
0.545
AC XY:
71665
AN XY:
131488
show subpopulations
Gnomad AFR exome
AF:
0.201
Gnomad AMR exome
AF:
0.703
Gnomad ASJ exome
AF:
0.460
Gnomad EAS exome
AF:
0.797
Gnomad SAS exome
AF:
0.590
Gnomad FIN exome
AF:
0.517
Gnomad NFE exome
AF:
0.508
Gnomad OTH exome
AF:
0.519
GnomAD4 exome
AF:
0.524
AC:
643554
AN:
1229008
Hom.:
173127
Cov.:
16
AF XY:
0.526
AC XY:
327720
AN XY:
622984
show subpopulations
Gnomad4 AFR exome
AF:
0.189
Gnomad4 AMR exome
AF:
0.695
Gnomad4 ASJ exome
AF:
0.460
Gnomad4 EAS exome
AF:
0.756
Gnomad4 SAS exome
AF:
0.596
Gnomad4 FIN exome
AF:
0.520
Gnomad4 NFE exome
AF:
0.513
Gnomad4 OTH exome
AF:
0.518
GnomAD4 genome
AF:
0.447
AC:
67840
AN:
151876
Hom.:
17097
Cov.:
31
AF XY:
0.453
AC XY:
33614
AN XY:
74212
show subpopulations
Gnomad4 AFR
AF:
0.206
Gnomad4 AMR
AF:
0.600
Gnomad4 ASJ
AF:
0.455
Gnomad4 EAS
AF:
0.773
Gnomad4 SAS
AF:
0.596
Gnomad4 FIN
AF:
0.523
Gnomad4 NFE
AF:
0.511
Gnomad4 OTH
AF:
0.484
Alfa
AF:
0.465
Hom.:
3588
Bravo
AF:
0.443
Asia WGS
AF:
0.619
AC:
2155
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
1.4
DANN
Benign
0.52
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs3740211; hg19: chr10-13370315; API