1-169730678-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000450.2(SELE):​c.530-61C>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
• Publications: 13 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELE	NM_000450.2	MANE Select	c.530-61C>T		intron	N/A	NP_000441.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELE	ENST00000333360.12	TSL:1 MANE Select	c.530-61C>T		intron	N/A	ENSP00000331736.7
	SELE	ENST00000367776.5	TSL:5	c.530-61C>T		intron	N/A	ENSP00000356750.1
	SELE	ENST00000367777.5	TSL:5	c.530-61C>T		intron	N/A	ENSP00000356751.1

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

African (AFR) AF: 0.267 AC: 4954 AN: 18574

American (AMR) AF: 0.328 AC: 5518 AN: 16812

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 6202 AN: 14108

East Asian (EAS) AF: 0.110 AC: 3190 AN: 29080

South Asian (SAS) AF: 0.334 AC: 7481 AN: 22374

European-Finnish (FIN) AF: 0.339 AC: 13529 AN: 39864

Middle Eastern (MID) AF: 0.460 AC: 1849 AN: 4022

European-Non Finnish (NFE) AF: 0.401 AC: 259199 AN: 645664

Other (OTH) AF: 0.379 AC: 13416 AN: 35412

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

African (AFR) AF: 0.283 AC: 11637 AN: 41150

American (AMR) AF: 0.377 AC: 5714 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1462 AN: 3460

East Asian (EAS) AF: 0.134 AC: 691 AN: 5154

South Asian (SAS) AF: 0.346 AC: 1654 AN: 4786

European-Finnish (FIN) AF: 0.347 AC: 3489 AN: 10044

Middle Eastern (MID) AF: 0.493 AC: 143 AN: 290

European-Non Finnish (NFE) AF: 0.413 AC: 27932 AN: 67706

Other (OTH) AF: 0.375 AC: 788 AN: 2100

Alfa AF: 0.394 Hom.: 37521

Bravo AF: 0.353

Asia WGS AF: 0.240 AC: 833 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.50
PhyloP100		0.082
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: rs3917419; hg19: chr1-169699819;