rs3917406

Positions:

• chr1-169733137-A-G
• chr1-169733137-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000450.2(SELE):​c.38-139T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 850,294 control chromosomes in the GnomAD database, including 35,064 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.30 (7403 hom., cov: 32)
  • Exomes 𝑓: 0.27 (27661 hom.)
• Consequence: SELE NM_000450.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.35

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]

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 1-169733137-A-G is Benign according to our data. Variant chr1-169733137-A-G is described in ClinVar as [Benign]. Clinvar id is 1684529.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SELE	NM_000450.2	c.38-139T>C		intron_variant		ENST00000333360.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELE	ENST00000333360.12	c.38-139T>C		intron_variant		1	NM_000450.2	P1

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45997 AN: 152006 Hom.: 7390 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.328

GnomAD4 exome AF: 0.267 AC: 186101 AN: 698170 Hom.: 27661 AF XY: 0.269 AC XY: 95482 AN XY: 354490

Gnomad4 AFR exome AF: 0.349

Gnomad4 AMR exome AF: 0.403

Gnomad4 ASJ exome AF: 0.321

Gnomad4 EAS exome AF: 0.535

Gnomad4 SAS exome AF: 0.346

Gnomad4 FIN exome AF: 0.315

Gnomad4 NFE exome AF: 0.230

Gnomad4 OTH exome AF: 0.290

GnomAD4 genome AF: 0.303 AC: 46057 AN: 152124 Hom.: 7403 Cov.: 32 AF XY: 0.307 AC XY: 22819 AN XY: 74358

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.330

Alfa AF: 0.274 Hom.: 906

Bravo AF: 0.313

Asia WGS AF: 0.395 AC: 1374 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Coronary artery disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

Rasad Genetic Department, Rasad Pathobiology and Genetic Laboratory

May 12, 2022

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.31

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: rs3917406; hg19: chr1-169702278;