chr10-100363286-G-C

Variant summary

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

The NM_005063.5(SCD):​c.*2353G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0379 in 152,382 control chromosomes in the GnomAD database, including 219 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 0.038 ( 219 hom., cov: 32)
Exomes 𝑓: 0.020 ( 0 hom. )

Consequence

SCD
NM_005063.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.355
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=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SCDNM_005063.5 linkuse as main transcriptc.*2353G>C 3_prime_UTR_variant 6/6 ENST00000370355.3 NP_005054.3 O00767

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SCDENST00000370355.3 linkuse as main transcriptc.*2353G>C 3_prime_UTR_variant 6/61 NM_005063.5 ENSP00000359380.2 O00767

Frequencies

GnomAD3 genomes
AF:
0.0379
AC:
5760
AN:
152166
Hom.:
220
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0784
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0265
Gnomad ASJ
AF:
0.00288
Gnomad EAS
AF:
0.110
Gnomad SAS
AF:
0.0760
Gnomad FIN
AF:
0.0636
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00633
Gnomad OTH
AF:
0.0253
GnomAD4 exome
AF:
0.0204
AC:
2
AN:
98
Hom.:
0
Cov.:
0
AF XY:
0.0303
AC XY:
2
AN XY:
66
show subpopulations
Gnomad4 AFR exome
AF:
0.125
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.500
Gnomad4 SAS exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0379
AC:
5772
AN:
152284
Hom.:
219
Cov.:
32
AF XY:
0.0412
AC XY:
3066
AN XY:
74464
show subpopulations
Gnomad4 AFR
AF:
0.0784
Gnomad4 AMR
AF:
0.0266
Gnomad4 ASJ
AF:
0.00288
Gnomad4 EAS
AF:
0.109
Gnomad4 SAS
AF:
0.0752
Gnomad4 FIN
AF:
0.0636
Gnomad4 NFE
AF:
0.00634
Gnomad4 OTH
AF:
0.0279
Alfa
AF:
0.00868
Hom.:
1
Bravo
AF:
0.0354
Asia WGS
AF:
0.116
AC:
403
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
5.1
DANN
Benign
0.55

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: rs560792; hg19: chr10-102123043; API