chr10-100362846-T-C

Variant names:

• chr10-100362846-T-C
• rs7849
• NM_005063.5:c.*1913T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005063.5(SCD):​c.*1913T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,176 control chromosomes in the GnomAD database, including 5,374 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 (5372 hom., cov: 32)
  • Exomes 𝑓: 0.27 (2 hom.)
• Consequence: SCD NM_005063.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.41
• Publications: 27 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) 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.*1913T>C		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.*1913T>C		3_prime_UTR_variant	Exon 6 of 6	1	NM_005063.5	ENSP00000359380.2

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36819 AN: 151998 Hom.: 5336 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.214

GnomAD4 exome AF: 0.267 AC: 16 AN: 60 Hom.: 2 Cov.: 0 AF XY: 0.269 AC XY: 14 AN XY: 52

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 2 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.190 AC: 8 AN: 42

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.243 AC: 36897 AN: 152116 Hom.: 5372 Cov.: 32 AF XY: 0.243 AC XY: 18082 AN XY: 74384

African (AFR) AF: 0.396 AC: 16405 AN: 41460

American (AMR) AF: 0.159 AC: 2429 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 754 AN: 3472

East Asian (EAS) AF: 0.230 AC: 1189 AN: 5172

South Asian (SAS) AF: 0.318 AC: 1531 AN: 4820

European-Finnish (FIN) AF: 0.182 AC: 1931 AN: 10592

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12021 AN: 67994

Other (OTH) AF: 0.215 AC: 455 AN: 2112

Alfa AF: 0.198 Hom.: 9236

Bravo AF: 0.244

Asia WGS AF: 0.296 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.12
DANN	Benign	0.54
PhyloP100		-4.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs7849; hg19: chr10-102122603;