rs41290540

Positions:

• chr10-100361805-A-C

Variant summary

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

The ENST00000370355.3(SCD):​c.*872A>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 0.0894 in 152,206 control chromosomes in the GnomAD database, including 653 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 0.089 (653 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SCD ENST00000370355.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCD	NM_005063.5	c.*872A>C		3_prime_UTR_variant	6/6	ENST00000370355.3	NP_005054.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCD	ENST00000370355.3	c.*872A>C		3_prime_UTR_variant	6/6	1	NM_005063.5	ENSP00000359380	P1

Frequencies

GnomAD3 genomes AF: 0.0894 AC: 13597 AN: 152088 Hom.: 650 Cov.: 32

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0653

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0732

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0789

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0894 AC: 13614 AN: 152206 Hom.: 653 Cov.: 32 AF XY: 0.0884 AC XY: 6577 AN XY: 74420

Gnomad4 AFR AF: 0.0892

Gnomad4 AMR AF: 0.0651

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0732

Gnomad4 NFE AF: 0.0931

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0908 Hom.: 137

Bravo AF: 0.0875

Asia WGS AF: 0.111 AC: 384 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.58
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.2

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: rs41290540; hg19: chr10-102121562;