15-45658944-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7

The NM_021199.4(SQOR):​c.21G>A​(p.Val7Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000165 in 1,570,246 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00081 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000095 ( 0 hom. )

Consequence

SQOR
NM_021199.4 synonymous

Scores

2

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.11
Variant links:
Genes affected
SQOR (HGNC:20390): (sulfide quinone oxidoreductase) The protein encoded by this gene may function in mitochondria to catalyze the conversion of sulfide to persulfides, thereby decreasing toxic concencrations of sulfide. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Sep 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 15-45658944-G-A is Benign according to our data. Variant chr15-45658944-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3357531.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=1.11 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SQORNM_021199.4 linkuse as main transcriptc.21G>A p.Val7Val synonymous_variant 2/10 ENST00000260324.12 NP_067022.1 Q9Y6N5A0A024R5X2
SQORNM_001271213.2 linkuse as main transcriptc.21G>A p.Val7Val synonymous_variant 3/11 NP_001258142.1 Q9Y6N5A0A024R5X2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SQORENST00000260324.12 linkuse as main transcriptc.21G>A p.Val7Val synonymous_variant 2/101 NM_021199.4 ENSP00000260324.7 Q9Y6N5
ENSG00000260170ENST00000564080.1 linkuse as main transcriptc.21G>A p.Val7Val synonymous_variant 2/63 ENSP00000455047.1 H3BNX3

Frequencies

GnomAD3 genomes
AF:
0.000815
AC:
124
AN:
152198
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00289
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000146
AC:
32
AN:
219318
Hom.:
0
AF XY:
0.0000839
AC XY:
10
AN XY:
119210
show subpopulations
Gnomad AFR exome
AF:
0.00186
Gnomad AMR exome
AF:
0.000132
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000117
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000952
AC:
135
AN:
1417930
Hom.:
0
Cov.:
32
AF XY:
0.0000816
AC XY:
57
AN XY:
698856
show subpopulations
Gnomad4 AFR exome
AF:
0.00332
Gnomad4 AMR exome
AF:
0.000221
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000130
Gnomad4 SAS exome
AF:
0.0000122
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.22e-7
Gnomad4 OTH exome
AF:
0.000189
GnomAD4 genome
AF:
0.000814
AC:
124
AN:
152316
Hom.:
0
Cov.:
32
AF XY:
0.000806
AC XY:
60
AN XY:
74478
show subpopulations
Gnomad4 AFR
AF:
0.00289
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000475
Hom.:
0
Bravo
AF:
0.000918

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

SQOR-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesJun 10, 2024This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
4.7
DANN
Benign
0.60

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: rs115371596; hg19: chr15-45951142; API