rs10883463

Variant names:

• chr10-100359197-T-C
• rs10883463
• NM_005063.5:c.881-1537T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-100359197-T-C
• chr10-100359197-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005063.5(SCD):​c.881-1537T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0719 in 152,208 control chromosomes in the GnomAD database, including 440 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 0.072 (440 hom., cov: 32)
• Consequence: SCD NM_005063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 17 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCD	NM_005063.5	c.881-1537T>C		intron_variant	Intron 5 of 5	ENST00000370355.3	NP_005054.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCD	ENST00000370355.3	c.881-1537T>C		intron_variant	Intron 5 of 5	1	NM_005063.5	ENSP00000359380.2

Frequencies

GnomAD3 genomes AF: 0.0719 AC: 10928 AN: 152090 Hom.: 439 Cov.: 32

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0493

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0454

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0750

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0719 AC: 10940 AN: 152208 Hom.: 440 Cov.: 32 AF XY: 0.0713 AC XY: 5308 AN XY: 74412

African (AFR) AF: 0.0822 AC: 3415 AN: 41522

American (AMR) AF: 0.0493 AC: 754 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 360 AN: 3470

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5168

South Asian (SAS) AF: 0.127 AC: 611 AN: 4824

European-Finnish (FIN) AF: 0.0454 AC: 481 AN: 10606

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0749 AC: 5097 AN: 68006

Other (OTH) AF: 0.0695 AC: 147 AN: 2114

Alfa AF: 0.0701 Hom.: 234

Bravo AF: 0.0715

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.029
DANN	Benign	0.44
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10883463; hg19: chr10-102118954;