rs3978768

Variant names:

• chr10-100361822-A-G
• rs3978768
• NM_005063.5:c.*889A>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.*889A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,086 control chromosomes in the GnomAD database, including 6,412 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 0.26 (6412 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SCD NM_005063.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCD	NM_005063.5	c.*889A>G		3_prime_UTR_variant	Exon 6 of 6	ENST00000370355.3	NP_005054.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCD	ENST00000370355.3	c.*889A>G		3_prime_UTR_variant	Exon 6 of 6	1	NM_005063.5	ENSP00000359380.2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39962 AN: 151968 Hom.: 6398 Cov.: 32

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.292

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.263 AC: 39987 AN: 152086 Hom.: 6412 Cov.: 32 AF XY: 0.261 AC XY: 19383 AN XY: 74320

African (AFR) AF: 0.0801 AC: 3326 AN: 41516

American (AMR) AF: 0.399 AC: 6086 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3468

East Asian (EAS) AF: 0.377 AC: 1953 AN: 5174

South Asian (SAS) AF: 0.183 AC: 883 AN: 4822

European-Finnish (FIN) AF: 0.262 AC: 2773 AN: 10574

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22938 AN: 67970

Other (OTH) AF: 0.292 AC: 614 AN: 2106

Alfa AF: 0.304 Hom.: 4097

Bravo AF: 0.272

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.9
DANN	Benign	0.82
PhyloP100		1.3
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)		0.0		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: rs3978768; hg19: chr10-102121579;