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GeneBe

10-100360777-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_005063.5(SCD):c.924C>T(p.Tyr308=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0041 in 1,613,978 control chromosomes in the GnomAD database, including 206 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.021 ( 108 hom., cov: 33)
Exomes 𝑓: 0.0024 ( 98 hom. )

Consequence

SCD
NM_005063.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.418
Variant links:
Genes affected
SCD (HGNC:10571): (stearoyl-CoA desaturase) This gene encodes an enzyme involved in fatty acid biosynthesis, primarily the synthesis of oleic acid. The protein belongs to the fatty acid desaturase family and is an integral membrane protein located in the endoplasmic reticulum. Transcripts of approximately 3.9 and 5.2 kb, differing only by alternative polyadenlyation signals, have been detected. A gene encoding a similar enzyme is located on chromosome 4 and a pseudogene of this gene is located on chromosome 17. [provided by RefSeq, Sep 2015]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 10-100360777-C-T is Benign according to our data. Variant chr10-100360777-C-T is described in ClinVar as [Benign]. Clinvar id is 773538.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.418 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0686 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SCDNM_005063.5 linkuse as main transcriptc.924C>T p.Tyr308= synonymous_variant 6/6 ENST00000370355.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SCDENST00000370355.3 linkuse as main transcriptc.924C>T p.Tyr308= synonymous_variant 6/61 NM_005063.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0208
AC:
3169
AN:
152204
Hom.:
107
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0707
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0110
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.0000941
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.000397
Gnomad OTH
AF:
0.0172
GnomAD3 exomes
AF:
0.00573
AC:
1439
AN:
251130
Hom.:
47
AF XY:
0.00429
AC XY:
582
AN XY:
135740
show subpopulations
Gnomad AFR exome
AF:
0.0749
Gnomad AMR exome
AF:
0.00425
Gnomad ASJ exome
AF:
0.000198
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.000362
Gnomad OTH exome
AF:
0.00440
GnomAD4 exome
AF:
0.00235
AC:
3438
AN:
1461656
Hom.:
98
Cov.:
31
AF XY:
0.00212
AC XY:
1539
AN XY:
727142
show subpopulations
Gnomad4 AFR exome
AF:
0.0744
Gnomad4 AMR exome
AF:
0.00494
Gnomad4 ASJ exome
AF:
0.0000765
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000209
Gnomad4 FIN exome
AF:
0.0000374
Gnomad4 NFE exome
AF:
0.000300
Gnomad4 OTH exome
AF:
0.00571
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0209
AC:
3178
AN:
152322
Hom.:
108
Cov.:
33
AF XY:
0.0201
AC XY:
1496
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.0707
Gnomad4 AMR
AF:
0.0110
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.0000941
Gnomad4 NFE
AF:
0.000397
Gnomad4 OTH
AF:
0.0170
Alfa
AF:
0.00988
Hom.:
21
Bravo
AF:
0.0245
Asia WGS
AF:
0.00375
AC:
13
AN:
3478
EpiCase
AF:
0.000436
EpiControl
AF:
0.000474

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.41
Cadd
Benign
11
Dann
Benign
0.87

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs61732512; hg19: chr10-102120534; API