chr10-100352318-A-G

Variant names:

• chr10-100352318-A-G
• rs11190480
• NM_005063.5:c.311-48A>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.311-48A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0976 in 1,590,678 control chromosomes in the GnomAD database, including 8,050 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 0.091 (682 hom., cov: 32)
  • Exomes 𝑓: 0.098 (7368 hom.)
• Consequence: SCD NM_005063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559
• Publications: 10 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005063.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCD	NM_005063.5	MANE Select	c.311-48A>G		intron	N/A	NP_005054.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCD	ENST00000370355.3	TSL:1 MANE Select	c.311-48A>G		intron	N/A	ENSP00000359380.2

Frequencies

GnomAD3 genomes AF: 0.0912 AC: 13874 AN: 152062 Hom.: 685 Cov.: 32

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0807

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0935

Gnomad OTH AF: 0.0837

GnomAD2 exomes AF: 0.0934 AC: 22735 AN: 243366 AF XY: 0.0966

Gnomad AFR exome AF: 0.0890

Gnomad AMR exome AF: 0.0454

Gnomad ASJ exome AF: 0.120

Gnomad EAS exome AF: 0.151

Gnomad FIN exome AF: 0.0754

Gnomad NFE exome AF: 0.0925

Gnomad OTH exome AF: 0.0870

GnomAD4 exome AF: 0.0983 AC: 141415 AN: 1438498 Hom.: 7368 Cov.: 28 AF XY: 0.0989 AC XY: 70562 AN XY: 713690

African (AFR) AF: 0.0883 AC: 2912 AN: 32992

American (AMR) AF: 0.0479 AC: 2088 AN: 43546

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 3058 AN: 25418

East Asian (EAS) AF: 0.151 AC: 5918 AN: 39274

South Asian (SAS) AF: 0.124 AC: 10519 AN: 84920

European-Finnish (FIN) AF: 0.0752 AC: 3857 AN: 51256

Middle Eastern (MID) AF: 0.107 AC: 478 AN: 4452

European-Non Finnish (NFE) AF: 0.0972 AC: 106612 AN: 1097284

Other (OTH) AF: 0.101 AC: 5973 AN: 59356

GnomAD4 genome AF: 0.0912 AC: 13877 AN: 152180 Hom.: 682 Cov.: 32 AF XY: 0.0906 AC XY: 6737 AN XY: 74400

African (AFR) AF: 0.0867 AC: 3601 AN: 41512

American (AMR) AF: 0.0659 AC: 1007 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3472

East Asian (EAS) AF: 0.155 AC: 800 AN: 5172

South Asian (SAS) AF: 0.123 AC: 593 AN: 4814

European-Finnish (FIN) AF: 0.0807 AC: 856 AN: 10604

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0935 AC: 6356 AN: 68002

Other (OTH) AF: 0.0837 AC: 177 AN: 2114

Alfa AF: 0.0958 Hom.: 352

Bravo AF: 0.0896

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.62
PhyloP100		-0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11190480; hg19: chr10-102112075; COSMIC: COSV107463482;