rs522951

Positions:

• chr10-100351144-G-C
• chr10-100351144-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005063.5(SCD):​c.311-1222G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,062 control chromosomes in the GnomAD database, including 29,006 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 0.60 (29006 hom., cov: 32)
• Consequence: SCD NM_005063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCD	NM_005063.5	c.311-1222G>C		intron_variant		ENST00000370355.3	NP_005054.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCD	ENST00000370355.3	c.311-1222G>C		intron_variant		1	NM_005063.5	ENSP00000359380	P1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91643 AN: 151944 Hom.: 28971 Cov.: 32

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.603 AC: 91723 AN: 152062 Hom.: 29006 Cov.: 32 AF XY: 0.609 AC XY: 45234 AN XY: 74324

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.575

Alfa AF: 0.437 Hom.: 1300

Bravo AF: 0.599

Asia WGS AF: 0.681 AC: 2369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.8
DANN	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs522951; hg19: chr10-102110901;