chr10-100365004-C-A

Variant names:

• chr10-100365004-C-A
• rs508384
• NM_005063.5:c.*4071C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005063.5(SCD):​c.*4071C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 151,880 control chromosomes in the GnomAD database, including 5,353 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 (5353 hom., cov: 31)
• Consequence: SCD NM_005063.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCD	NM_005063.5	c.*4071C>A		downstream_gene_variant		ENST00000370355.3	NP_005054.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCD	ENST00000370355.3	c.*4071C>A		downstream_gene_variant		1	NM_005063.5	ENSP00000359380.2

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36761 AN: 151762 Hom.: 5317 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.243 AC: 36839 AN: 151880 Hom.: 5353 Cov.: 31 AF XY: 0.243 AC XY: 18035 AN XY: 74240

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.214

Alfa AF: 0.172 Hom.: 2494

Bravo AF: 0.244

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.4
DANN	Benign	0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs508384; hg19: chr10-102124761;