dbSNP rs3071: SCD:c.647+74A>C (chr10-100354706-A-C) – 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.647+74A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 1,149,876 control chromosomes in the GnomAD database, including 50,783 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 0.24 ( 5535 hom., cov: 32)

Exomes 𝑓: 0.29 ( 45248 hom. )

Consequence

SCD
NM_005063.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.365

Publications

22 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCD	NM_005063.5 link	c.647+74A>C		intron_variant	Intron 4 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.647+74A>C		intron_variant	Intron 4 of 5	1	NM_005063.5	ENSP00000359380.2		O00767

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36498

AN:

151952

Hom.:

5537

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0557

Gnomad AMI

AF:

0.375

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.337

Gnomad SAS

AF:

0.301

Gnomad FIN

AF:

0.403

Gnomad MID

AF:

0.220

Gnomad NFE

AF:

0.308

Gnomad OTH

AF:

0.246

GnomAD4 exome

AF:

0.295

AC:

294261

AN:

997804

Hom.:

45248

AF XY:

0.296

AC XY:

150769

AN XY:

509052

show subpopulations

African (AFR)

AF:

0.0470

AC:

1116

AN:

23720

American (AMR)

AF:

0.263

AC:

9348

AN:

35508

Ashkenazi Jewish (ASJ)

AF:

0.235

AC:

5127

AN:

21796

East Asian (EAS)

AF:

0.300

AC:

11116

AN:

37056

South Asian (SAS)

AF:

0.297

AC:

21384

AN:

72068

European-Finnish (FIN)

AF:

0.399

AC:

20499

AN:

51406

Middle Eastern (MID)

AF:

0.213

AC:

1034

AN:

4858

European-Non Finnish (NFE)

AF:

0.301

AC:

212444

AN:

706750

Other (OTH)

AF:

0.273

AC:

12193

AN:

44642

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

10535

21070

31605

42140

52675

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5606

11212

16818

22424

28030

<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:

0.240

AC:

36496

AN:

152072

Hom.:

5535

Cov.:

AF XY:

0.247

AC XY:

18362

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.0556

AC:

2307

AN:

41524

American (AMR)

AF:

0.264

AC:

4026

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.241

AC:

835

AN:

3468

East Asian (EAS)

AF:

0.336

AC:

1738

AN:

5168

South Asian (SAS)

AF:

0.302

AC:

1454

AN:

4818

European-Finnish (FIN)

AF:

0.403

AC:

4251

AN:

10560

Middle Eastern (MID)

AF:

0.226

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.308

AC:

20960

AN:

67950

Other (OTH)

AF:

0.246

AC:

518

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1315

2630

3946

5261

6576

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

390

780

1170

1560

1950

<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:

0.237

Hom.:

2077

Bravo

AF:

0.218

Asia WGS

AF:

0.307

AC:

1066

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.8

(source)

DANN

Benign

0.47

PhyloP100

-0.36

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)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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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