rs2235304

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003005.4(SELP):​c.1148-826C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 152,106 control chromosomes in the GnomAD database, including 399 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 0.060 ( 399 hom., cov: 32)

Consequence

SELP
NM_003005.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.84
Variant links:
Genes affected
SELP (HGNC:10721): (selectin P) This gene encodes a 140 kDa protein that is stored in the alpha-granules of platelets and Weibel-Palade bodies of endothelial cells. This protein redistributes to the plasma membrane during platelet activation and degranulation and mediates the interaction of activated endothelial cells or platelets with leukocytes. The membrane protein is a calcium-dependent receptor that binds to sialylated forms of Lewis blood group carbohydrate antigens on neutrophils and monocytes. Alternative splice variants may occur but are not well documented. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SELPNM_003005.4 linkc.1148-826C>T intron_variant Intron 7 of 16 ENST00000263686.11 NP_002996.2 P16109Q6NUL9A0A024R8Y9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SELPENST00000263686.11 linkc.1148-826C>T intron_variant Intron 7 of 16 1 NM_003005.4 ENSP00000263686.5 P16109

Frequencies

GnomAD3 genomes
AF:
0.0597
AC:
9069
AN:
151988
Hom.:
400
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0238
Gnomad AMI
AF:
0.0274
Gnomad AMR
AF:
0.0498
Gnomad ASJ
AF:
0.119
Gnomad EAS
AF:
0.195
Gnomad SAS
AF:
0.0916
Gnomad FIN
AF:
0.0825
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.0644
Gnomad OTH
AF:
0.0736
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0596
AC:
9063
AN:
152106
Hom.:
399
Cov.:
32
AF XY:
0.0608
AC XY:
4520
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.0237
Gnomad4 AMR
AF:
0.0497
Gnomad4 ASJ
AF:
0.119
Gnomad4 EAS
AF:
0.194
Gnomad4 SAS
AF:
0.0925
Gnomad4 FIN
AF:
0.0825
Gnomad4 NFE
AF:
0.0644
Gnomad4 OTH
AF:
0.0714
Alfa
AF:
0.0635
Hom.:
99
Bravo
AF:
0.0561
Asia WGS
AF:
0.144
AC:
500
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.77
DANN
Benign
0.30

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2235304; hg19: chr1-169579753; API