NM_005063.5:c.648-515G>T

Variant names:

• chr10-100356017-G-T
• rs3793768
• NM_005063.5:c.648-515G>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.648-515G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,996 control chromosomes in the GnomAD database, including 12,790 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 0.41 (12790 hom., cov: 32)
• Consequence: SCD NM_005063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005063.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCD	NM_005063.5	MANE Select	c.648-515G>T		intron	N/A	NP_005054.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCD	ENST00000370355.3	TSL:1 MANE Select	c.648-515G>T		intron	N/A	ENSP00000359380.2

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62076 AN: 151876 Hom.: 12774 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.409 AC: 62137 AN: 151996 Hom.: 12790 Cov.: 32 AF XY: 0.404 AC XY: 30027 AN XY: 74310

African (AFR) AF: 0.394 AC: 16349 AN: 41446

American (AMR) AF: 0.492 AC: 7519 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1543 AN: 3464

East Asian (EAS) AF: 0.379 AC: 1956 AN: 5164

South Asian (SAS) AF: 0.289 AC: 1392 AN: 4812

European-Finnish (FIN) AF: 0.370 AC: 3911 AN: 10562

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.413 AC: 28093 AN: 67946

Other (OTH) AF: 0.440 AC: 928 AN: 2108

Alfa AF: 0.340 Hom.: 1534

Bravo AF: 0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.70
DANN	Benign	0.56
PhyloP100		-1.2
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: rs3793768; hg19: chr10-102115774;