chr4-82649098-A-G

Position:

• chr4-82649098-A-G

Variant summary

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

The NM_001037582.3(SCD5):​c.570-12275T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 151,404 control chromosomes in the GnomAD database, including 44,463 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 0.76 (44463 hom., cov: 28)
• Consequence: SCD5 NM_001037582.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699

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 (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCD5	NM_001037582.3	c.570-12275T>C		intron_variant		ENST00000319540.9	NP_001032671.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCD5	ENST00000319540.9	c.570-12275T>C		intron_variant		1	NM_001037582.3	ENSP00000316329.4

Frequencies

GnomAD3 genomes AF: 0.759 AC: 114835 AN: 151288 Hom.: 44442 Cov.: 28

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.759 AC: 114895 AN: 151404 Hom.: 44463 Cov.: 28 AF XY: 0.757 AC XY: 55937 AN XY: 73886

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.780

Alfa AF: 0.798 Hom.: 25780

Bravo AF: 0.761

Asia WGS AF: 0.843 AC: 2934 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	0.087
DANN	Benign	0.67

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: rs4459983; hg19: chr4-83570251;