rs1980360

Positions:

• chr4-82773130-G-A
• chr4-82773130-G-C
• chr4-82773130-G-T

Variant summary

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

The NM_001037582.3(SCD5):​c.232+25176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,948 control chromosomes in the GnomAD database, including 20,584 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 0.47 (20584 hom., cov: 31)
• Consequence: SCD5 NM_001037582.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

Genes affected

SCD5 (HGNC:21088): (stearoyl-CoA desaturase 5) Stearoyl-CoA desaturase (SCD; EC 1.14.99.5) is an integral membrane protein of the endoplasmic reticulum that catalyzes the formation of monounsaturated fatty acids from saturated fatty acids. SCD may be a key regulator of energy metabolism with a role in obesity and dislipidemia. Four SCD isoforms, Scd1 through Scd4, have been identified in mouse. In contrast, only 2 SCD isoforms, SCD1 (MIM 604031) and SCD5, have been identified in human. SCD1 shares about 85% amino acid identity with all 4 mouse SCD isoforms, as well as with rat Scd1 and Scd2. In contrast, SCD5 shares limited homology with the rodent SCDs and appears to be unique to primates (Wang et al., 2005 [PubMed 15907797]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCD5	NM_001037582.3	c.232+25176C>T		intron_variant		ENST00000319540.9	NP_001032671.2
SCD5	NM_024906.3	c.232+25176C>T		intron_variant			NP_079182.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCD5	ENST00000319540.9	c.232+25176C>T		intron_variant		1	NM_001037582.3	ENSP00000316329.4
SCD5	ENST00000273908.4	c.232+25176C>T		intron_variant		2		ENSP00000273908.4

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71340 AN: 151830 Hom.: 20574 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.470 AC: 71364 AN: 151948 Hom.: 20584 Cov.: 31 AF XY: 0.472 AC XY: 35054 AN XY: 74248

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.541

Alfa AF: 0.589 Hom.: 37035

Bravo AF: 0.460

Asia WGS AF: 0.405 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.48
DANN	Benign	0.63

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

Other links and lift over

dbSNP: rs1980360; hg19: chr4-83694283;