rs10883465

Variant summary

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

The NM_005063.5(SCD):​c.*1497C>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 0.234 in 152,018 control chromosomes in the GnomAD database, including 4,893 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 0.23 ( 4893 hom., cov: 32)
Exomes 𝑓: 0.14 ( 0 hom. )

Consequence

SCD
NM_005063.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.727
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SCDNM_005063.5 linkuse as main transcriptc.*1497C>G 3_prime_UTR_variant 6/6 ENST00000370355.3 NP_005054.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SCDENST00000370355.3 linkuse as main transcriptc.*1497C>G 3_prime_UTR_variant 6/61 NM_005063.5 ENSP00000359380 P1

Frequencies

GnomAD3 genomes
AF:
0.234
AC:
35544
AN:
151886
Hom.:
4863
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.365
Gnomad AMI
AF:
0.117
Gnomad AMR
AF:
0.156
Gnomad ASJ
AF:
0.217
Gnomad EAS
AF:
0.239
Gnomad SAS
AF:
0.319
Gnomad FIN
AF:
0.182
Gnomad MID
AF:
0.250
Gnomad NFE
AF:
0.177
Gnomad OTH
AF:
0.209
GnomAD4 exome
AF:
0.143
AC:
2
AN:
14
Hom.:
0
Cov.:
0
AF XY:
0.200
AC XY:
2
AN XY:
10
show subpopulations
Gnomad4 NFE exome
AF:
0.167
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.234
AC:
35615
AN:
152004
Hom.:
4893
Cov.:
32
AF XY:
0.235
AC XY:
17475
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.366
Gnomad4 AMR
AF:
0.156
Gnomad4 ASJ
AF:
0.217
Gnomad4 EAS
AF:
0.238
Gnomad4 SAS
AF:
0.317
Gnomad4 FIN
AF:
0.182
Gnomad4 NFE
AF:
0.176
Gnomad4 OTH
AF:
0.210
Alfa
AF:
0.206
Hom.:
447
Bravo
AF:
0.234
Asia WGS
AF:
0.294
AC:
1025
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
5.1
DANN
Benign
0.56
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: rs10883465; hg19: chr10-102122187; API