rs7904902

Positions:

• chr10-100353901-G-A

Variant summary

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

The NM_005063.5(SCD):​c.442-526G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0763 in 152,270 control chromosomes in the GnomAD database, including 1,272 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 0.076 (1272 hom., cov: 33)
• Consequence: SCD NM_005063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCD	NM_005063.5	c.442-526G>A		intron_variant		ENST00000370355.3	NP_005054.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCD	ENST00000370355.3	c.442-526G>A		intron_variant		1	NM_005063.5	ENSP00000359380.2

Frequencies

GnomAD3 genomes AF: 0.0762 AC: 11591 AN: 152152 Hom.: 1271 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0270

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.0694

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00459

Gnomad OTH AF: 0.0555

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

GnomAD4 genome AF: 0.0763 AC: 11614 AN: 152270 Hom.: 1272 Cov.: 33 AF XY: 0.0742 AC XY: 5525 AN XY: 74472

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.0269

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.0286

Gnomad4 SAS AF: 0.0696

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00459

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0533 Hom.: 231

Bravo AF: 0.0835

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.36
DANN	Benign	0.61

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: rs7904902; hg19: chr10-102113658;