rs1502593

chr10-100349445-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.310+1099G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,060 control chromosomes in the GnomAD database, including 9,423 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 0.34 (9423 hom., cov: 32)
• Consequence: SCD NM_005063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCD	NM_005063.5	c.310+1099G>A		intron_variant		ENST00000370355.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCD	ENST00000370355.3	c.310+1099G>A		intron_variant		1	NM_005063.5	P1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51481 AN: 151944 Hom.: 9427 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.339 AC: 51479 AN: 152060 Hom.: 9423 Cov.: 32 AF XY: 0.346 AC XY: 25702 AN XY: 74310

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.356

Alfa AF: 0.389 Hom.: 16147

Bravo AF: 0.320

Asia WGS AF: 0.339 AC: 1179 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	0.20
Dann	Benign	0.50

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: rs1502593; hg19: chr10-102109202;