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GeneBe

1-169593711-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_003005.4(SELP):c.2301T>C(p.Thr767=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00216 in 1,613,510 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.010 ( 26 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 31 hom. )

Consequence

SELP
NM_003005.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.663
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 -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-169593711-A-G is Benign according to our data. Variant chr1-169593711-A-G is described in ClinVar as [Benign]. Clinvar id is 775623.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.663 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0105 (1596/152332) while in subpopulation AFR AF= 0.035 (1456/41566). AF 95% confidence interval is 0.0335. There are 26 homozygotes in gnomad4. There are 756 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 26 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SELPNM_003005.4 linkuse as main transcriptc.2301T>C p.Thr767= synonymous_variant 14/17 ENST00000263686.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SELPENST00000263686.11 linkuse as main transcriptc.2301T>C p.Thr767= synonymous_variant 14/171 NM_003005.4 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0105
AC:
1597
AN:
152214
Hom.:
26
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0351
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00740
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000413
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000162
Gnomad OTH
AF:
0.00766
GnomAD3 exomes
AF:
0.00297
AC:
746
AN:
250996
Hom.:
12
AF XY:
0.00220
AC XY:
299
AN XY:
135700
show subpopulations
Gnomad AFR exome
AF:
0.0375
Gnomad AMR exome
AF:
0.00281
Gnomad ASJ exome
AF:
0.0000995
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000211
Gnomad OTH exome
AF:
0.00180
GnomAD4 exome
AF:
0.00129
AC:
1887
AN:
1461178
Hom.:
31
Cov.:
31
AF XY:
0.00110
AC XY:
799
AN XY:
726912
show subpopulations
Gnomad4 AFR exome
AF:
0.0380
Gnomad4 AMR exome
AF:
0.00289
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000696
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000291
Gnomad4 OTH exome
AF:
0.00247
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0105
AC:
1596
AN:
152332
Hom.:
26
Cov.:
32
AF XY:
0.0101
AC XY:
756
AN XY:
74500
show subpopulations
Gnomad4 AFR
AF:
0.0350
Gnomad4 AMR
AF:
0.00739
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000162
Gnomad4 OTH
AF:
0.00758
Alfa
AF:
0.00322
Hom.:
9
Bravo
AF:
0.0118
Asia WGS
AF:
0.00260
AC:
9
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJun 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
Cadd
Benign
0.89
Dann
Benign
0.38

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: rs3917831; hg19: chr1-169562949; API