1-169731361-T-C

Position:

• chr1-169731361-T-C

Variant summary

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

The NM_000450.2(SELE):​c.529+474A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,966 control chromosomes in the GnomAD database, including 48,806 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 0.79 (48593 hom., cov: 31)
  • Exomes 𝑓: 0.71 (213 hom.)
• Consequence: SELE NM_000450.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

SELE (HGNC:10718): (selectin E) The protein encoded by this gene is found in cytokine-stimulated endothelial cells and is thought to be responsible for the accumulation of blood leukocytes at sites of inflammation by mediating the adhesion of cells to the vascular lining. It exhibits structural features such as the presence of lectin- and EGF-like domains followed by short consensus repeat (SCR) domains that contain 6 conserved cysteine residues. These proteins are part of the selectin family of cell adhesion molecules. Adhesion molecules participate in the interaction between leukocytes and the endothelium and appear to be involved in the pathogenesis of atherosclerosis. [provided by RefSeq, Jul 2008]

C1orf112 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SELE	NM_000450.2	c.529+474A>G		intron_variant		ENST00000333360.12	NP_000441.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SELE	ENST00000333360.12	c.529+474A>G		intron_variant		1	NM_000450.2	ENSP00000331736.7

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120541 AN: 152026 Hom.: 48536 Cov.: 31

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.799

GnomAD4 exome AF: 0.714 AC: 587 AN: 822 Hom.: 213 AF XY: 0.728 AC XY: 271 AN XY: 372

Gnomad4 AMR exome AF: 0.830

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.773

Gnomad4 FIN exome AF: 0.600

Gnomad4 NFE exome AF: 0.692

Gnomad4 OTH exome AF: 0.824

GnomAD4 genome AF: 0.793 AC: 120657 AN: 152144 Hom.: 48593 Cov.: 31 AF XY: 0.792 AC XY: 58884 AN XY: 74360

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.797

Alfa AF: 0.728 Hom.: 4423

Bravo AF: 0.806

Asia WGS AF: 0.768 AC: 2668 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.32

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

Publications

LitVar

Other links and lift over

dbSNP: rs3917412; hg19: chr1-169700502;