chr10-100363286-G-C

Variant names:

• chr10-100363286-G-C
• rs560792
• NM_005063.5:c.*2353G>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 9 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 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.*2353G>C		3_prime_UTR	Exon 6 of 6	NP_005054.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCD	ENST00000370355.3	TSL:1 MANE Select	c.*2353G>C		3_prime_UTR	Exon 6 of 6	ENSP00000359380.2

Frequencies

GnomAD3 genomes AF: 0.0379 AC: 5760 AN: 152166 Hom.: 220 Cov.: 32

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

African (AFR) AF: 0.125 AC: 1 AN: 8

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 74

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.0379 AC: 5772 AN: 152284 Hom.: 219 Cov.: 32 AF XY: 0.0412 AC XY: 3066 AN XY: 74464

African (AFR) AF: 0.0784 AC: 3258 AN: 41530

American (AMR) AF: 0.0266 AC: 407 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3472

East Asian (EAS) AF: 0.109 AC: 567 AN: 5180

South Asian (SAS) AF: 0.0752 AC: 363 AN: 4828

European-Finnish (FIN) AF: 0.0636 AC: 675 AN: 10616

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00634 AC: 431 AN: 68030

Other (OTH) AF: 0.0279 AC: 59 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.1
DANN	Benign	0.55
PhyloP100		0.35
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: rs560792; hg19: chr10-102123043;