rs2167444

Variant names:

• chr10-100364987-T-A
• rs2167444
• NM_005063.5:c.*4054T>A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_005063.5(SCD):​c.*4054T>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,126 control chromosomes in the GnomAD database, including 1,751 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 0.14 (1751 hom., cov: 31)
• Consequence: SCD NM_005063.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97

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=-0.31).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCD	NM_005063.5	c.*4054T>A		downstream_gene_variant		ENST00000370355.3	NP_005054.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCD	ENST00000370355.3	c.*4054T>A		downstream_gene_variant		1	NM_005063.5	ENSP00000359380.2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21862 AN: 152008 Hom.: 1747 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.135

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.144 AC: 21876 AN: 152126 Hom.: 1751 Cov.: 31 AF XY: 0.143 AC XY: 10622 AN XY: 74382

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.135

Alfa AF: 0.151 Hom.: 227

Bravo AF: 0.139

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	19
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2167444; hg19: chr10-102124744;