dbSNP rs11190480: SCD:c.311-48A>G (chr10-100352318-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.559

Publications

10 publications found

Variant links:

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]

SCD links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCD	NM_005063.5 link	c.311-48A>G		intron_variant	Intron 2 of 5	ENST00000370355.3	NP_005054.3	O00767

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCD	ENST00000370355.3 link	c.311-48A>G		intron_variant	Intron 2 of 5	1	NM_005063.5	ENSP00000359380.2		O00767

Frequencies

GnomAD3 genomes

AF:

0.0912

AC:

13874

AN:

152062

Hom.:

685

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.0989

AC XY:

70562

AN XY:

713690

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

5806

11612

17419

23225

29031

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4076

8152

12228

16304

20380

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0912

AC:

13877

AN:

152180

Hom.:

682

Cov.:

AF XY:

0.0906

AC XY:

6737

AN XY:

74400

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0935

AC:

6356

AN:

68002

Other (OTH)

AF:

0.0837

AC:

177

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

644

1288

1931

2575

3219

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.5

(source)

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)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over