rs522951

Variant names:

• chr10-100351144-G-C
• rs522951
• NM_005063.5:c.311-1222G>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 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=-0.88).
• 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 rank	MANE	Protein	UniProt
SCD	NM_005063.5	c.311-1222G>C		intron_variant	Intron 2 of 5	ENST00000370355.3	NP_005054.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCD	ENST00000370355.3	c.311-1222G>C		intron_variant	Intron 2 of 5	1	NM_005063.5	ENSP00000359380.2

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

African (AFR) AF: 0.803 AC: 33338 AN: 41510

American (AMR) AF: 0.499 AC: 7624 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1726 AN: 3468

East Asian (EAS) AF: 0.652 AC: 3378 AN: 5184

South Asian (SAS) AF: 0.672 AC: 3237 AN: 4816

European-Finnish (FIN) AF: 0.599 AC: 6318 AN: 10554

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34201 AN: 67942

Other (OTH) AF: 0.575 AC: 1213 AN: 2108

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
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs522951; hg19: chr10-102110901;