10-100347540-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_005063.5(SCD):c.27+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00831 in 1,613,876 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0066 (4 hom., cov: 32)
  • Exomes 𝑓: 0.0085 (62 hom.)
• Consequence: SCD NM_005063.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.933

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BP6: Variant 10-100347540-C-T is Benign according to our data. Variant chr10-100347540-C-T is described in ClinVar as [Benign]. Clinvar id is 781943.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd at 1006 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCD	NM_005063.5	c.27+9C>T		intron_variant		ENST00000370355.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCD	ENST00000370355.3	c.27+9C>T		intron_variant		1	NM_005063.5	P1

Frequencies

GnomAD3 genomes AF: 0.00661 AC: 1006 AN: 152210 Hom.: 4 Cov.: 32

Gnomad AFR AF: 0.00157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00884

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00869

Gnomad OTH AF: 0.00574

GnomAD3 exomes AF: 0.00706 AC: 1746 AN: 247292 Hom.: 8 AF XY: 0.00689 AC XY: 926 AN XY: 134322

Gnomad AFR exome AF: 0.00107

Gnomad AMR exome AF: 0.00391

Gnomad ASJ exome AF: 0.0101

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00255

Gnomad FIN exome AF: 0.0135

Gnomad NFE exome AF: 0.00991

Gnomad OTH exome AF: 0.00525

GnomAD4 exome AF: 0.00849 AC: 12403 AN: 1461548 Hom.: 62 Cov.: 34 AF XY: 0.00823 AC XY: 5986 AN XY: 727090

Gnomad4 AFR exome AF: 0.00105

Gnomad4 AMR exome AF: 0.00378

Gnomad4 ASJ exome AF: 0.0105

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00253

Gnomad4 FIN exome AF: 0.0125

Gnomad4 NFE exome AF: 0.00947

Gnomad4 OTH exome AF: 0.00828

GnomAD4 genome AF: 0.00660 AC: 1006 AN: 152328 Hom.: 4 Cov.: 32 AF XY: 0.00685 AC XY: 510 AN XY: 74486

Gnomad4 AFR AF: 0.00156

Gnomad4 AMR AF: 0.00882

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00186

Gnomad4 FIN AF: 0.0147

Gnomad4 NFE AF: 0.00869

Gnomad4 OTH AF: 0.00568

Alfa AF: 0.00697 Hom.: 0

Bravo AF: 0.00561

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	15
Dann	Benign	0.93

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: rs201033598; hg19: chr10-102107297;