1-169730921-C-T

Variant names:

• chr1-169730921-C-T
• rs3917417
• NM_000450.2:c.530-304G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000450.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELE	NM_000450.2	MANE Select	c.530-304G>A		intron	N/A	NP_000441.2	P16581

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELE	ENST00000333360.12	TSL:1 MANE Select	c.530-304G>A		intron	N/A	ENSP00000331736.7	P16581
	SELE	ENST00000367776.5	TSL:5	c.530-304G>A		intron	N/A	ENSP00000356750.1	Q5TI73
	SELE	ENST00000367777.5	TSL:5	c.530-304G>A		intron	N/A	ENSP00000356751.1	Q5TI74

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

African (AFR) AF: 0.0391 AC: 1622 AN: 41534

American (AMR) AF: 0.0643 AC: 983 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3470

East Asian (EAS) AF: 0.0170 AC: 88 AN: 5190

South Asian (SAS) AF: 0.0746 AC: 360 AN: 4824

European-Finnish (FIN) AF: 0.0716 AC: 758 AN: 10582

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.106 AC: 7210 AN: 67980

Other (OTH) AF: 0.0841 AC: 178 AN: 2116

Alfa AF: 0.0374 Hom.: 39

Bravo AF: 0.0748

Asia WGS AF: 0.0460 AC: 161 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.28
PhyloP100		-0.26
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: rs3917417; hg19: chr1-169700062;