1-169621926-T-C

Variant summary

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

The NM_003005.4(SELP):​c.4-2707A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,122 control chromosomes in the GnomAD database, including 5,102 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 0.21 ( 5102 hom., cov: 33)

Consequence

SELP
NM_003005.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.375
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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SELPNM_003005.4 linkuse as main transcriptc.4-2707A>G intron_variant ENST00000263686.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SELPENST00000263686.11 linkuse as main transcriptc.4-2707A>G intron_variant 1 NM_003005.4 P1

Frequencies

GnomAD3 genomes
AF:
0.211
AC:
32016
AN:
152004
Hom.:
5077
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.449
Gnomad AMI
AF:
0.103
Gnomad AMR
AF:
0.181
Gnomad ASJ
AF:
0.103
Gnomad EAS
AF:
0.137
Gnomad SAS
AF:
0.130
Gnomad FIN
AF:
0.132
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.104
Gnomad OTH
AF:
0.176
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.211
AC:
32095
AN:
152122
Hom.:
5102
Cov.:
33
AF XY:
0.212
AC XY:
15765
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.450
Gnomad4 AMR
AF:
0.182
Gnomad4 ASJ
AF:
0.103
Gnomad4 EAS
AF:
0.137
Gnomad4 SAS
AF:
0.129
Gnomad4 FIN
AF:
0.132
Gnomad4 NFE
AF:
0.104
Gnomad4 OTH
AF:
0.175
Alfa
AF:
0.124
Hom.:
1528
Bravo
AF:
0.225
Asia WGS
AF:
0.146
AC:
507
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
3.9
DANN
Benign
0.72

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: rs3917686; hg19: chr1-169591164; API