NM_000450.2:c.530-61C>T

Variant names:

• chr1-169730678-G-A
• rs3917419
• NM_000450.2:c.530-61C>T

Variant summary

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

The NM_000450.2(SELE):​c.530-61C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 976,674 control chromosomes in the GnomAD database, including 74,031 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 0.36 (9979 hom., cov: 30)
  • Exomes 𝑓: 0.38 (64052 hom.)
• Consequence: SELE NM_000450.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

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:25565): (FIGNL1 interacting regulator of recombination and mitosis)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELE	NM_000450.2	c.530-61C>T		intron_variant	Intron 4 of 13	ENST00000333360.12	NP_000441.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELE	ENST00000333360.12	c.530-61C>T		intron_variant	Intron 4 of 13	1	NM_000450.2	ENSP00000331736.7

Frequencies

GnomAD3 genomes AF: 0.357 AC: 53822 AN: 150668 Hom.: 9980 Cov.: 30

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.379

GnomAD4 exome AF: 0.382 AC: 315338 AN: 825910 Hom.: 64052 AF XY: 0.384 AC XY: 155851 AN XY: 406096

Gnomad4 AFR exome AF: 0.267

Gnomad4 AMR exome AF: 0.328

Gnomad4 ASJ exome AF: 0.440

Gnomad4 EAS exome AF: 0.110

Gnomad4 SAS exome AF: 0.334

Gnomad4 FIN exome AF: 0.339

Gnomad4 NFE exome AF: 0.401

Gnomad4 OTH exome AF: 0.379

GnomAD4 genome AF: 0.357 AC: 53828 AN: 150764 Hom.: 9979 Cov.: 30 AF XY: 0.353 AC XY: 26005 AN XY: 73576

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.375

Alfa AF: 0.403 Hom.: 25287

Bravo AF: 0.353

Asia WGS AF: 0.240 AC: 833 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.50

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: rs3917419; hg19: chr1-169699819;