NM_005063.5:c.442-535C>T

Variant names:

• chr10-100353892-C-T
• rs11190483
• NM_005063.5:c.442-535C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005063.5(SCD):​c.442-535C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,110 control chromosomes in the GnomAD database, including 5,364 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 0.24 (5364 hom., cov: 33)
• Consequence: SCD NM_005063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 8 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCD	NM_005063.5	c.442-535C>T		intron_variant	Intron 3 of 5	ENST00000370355.3	NP_005054.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCD	ENST00000370355.3	c.442-535C>T		intron_variant	Intron 3 of 5	1	NM_005063.5	ENSP00000359380.2

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35921 AN: 151992 Hom.: 5367 Cov.: 33

Gnomad AFR AF: 0.0547

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.244

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.236 AC: 35916 AN: 152110 Hom.: 5364 Cov.: 33 AF XY: 0.244 AC XY: 18108 AN XY: 74342

African (AFR) AF: 0.0546 AC: 2267 AN: 41536

American (AMR) AF: 0.260 AC: 3969 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 792 AN: 3468

East Asian (EAS) AF: 0.336 AC: 1736 AN: 5162

South Asian (SAS) AF: 0.302 AC: 1457 AN: 4824

European-Finnish (FIN) AF: 0.399 AC: 4208 AN: 10556

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.303 AC: 20572 AN: 67964

Other (OTH) AF: 0.243 AC: 513 AN: 2112

Alfa AF: 0.262 Hom.: 11070

Bravo AF: 0.214

Asia WGS AF: 0.305 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.71
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11190483; hg19: chr10-102113649;