chr1-169730921-C-T

Position:

• chr1-169730921-C-T

Variant summary

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

The NM_000450.2(SELE):​c.530-304G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 152,188 control chromosomes in the GnomAD database, including 552 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 0.078 (552 hom., cov: 31)
• Consequence: SELE NM_000450.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SELE	NM_000450.2	c.530-304G>A		intron_variant		ENST00000333360.12	NP_000441.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SELE	ENST00000333360.12	c.530-304G>A		intron_variant		1	NM_000450.2	ENSP00000331736.7

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11841 AN: 152070 Hom.: 552 Cov.: 31

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.0746

Gnomad FIN AF: 0.0716

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0860

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

GnomAD4 genome AF: 0.0778 AC: 11843 AN: 152188 Hom.: 552 Cov.: 31 AF XY: 0.0755 AC XY: 5620 AN XY: 74404

Gnomad4 AFR AF: 0.0391

Gnomad4 AMR AF: 0.0643

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0170

Gnomad4 SAS AF: 0.0746

Gnomad4 FIN AF: 0.0716

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0841

Alfa AF: 0.0370 Hom.: 39

Bravo AF: 0.0748

Asia WGS AF: 0.0460 AC: 161 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.28

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: rs3917417; hg19: chr1-169700062;