Genetic Variant NM_003005.4:c.2288-100C>T (chr1-169593824-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003005.4(SELP):c.2288-100C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0878 in 1,163,380 control chromosomes in the GnomAD database, including 4,845 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 0.067 ( 447 hom., cov: 32)

Exomes 𝑓: 0.091 ( 4398 hom. )

Consequence

SELP
NM_003005.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.986

Publications

7 publications found

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]

SELP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.099 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELP	NM_003005.4 link	c.2288-100C>T		intron_variant	Intron 13 of 16	ENST00000263686.11	NP_002996.2	P16109Q6NUL9A0A024R8Y9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELP	ENST00000263686.11 link	c.2288-100C>T		intron_variant	Intron 13 of 16	1	NM_003005.4	ENSP00000263686.5		P16109

Frequencies

GnomAD3 genomes

AF:

0.0670

AC:

10190

AN:

152068

Hom.:

446

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0184

Gnomad AMI

AF:

0.122

Gnomad AMR

AF:

0.0634

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.00731

Gnomad SAS

AF:

0.0403

Gnomad FIN

AF:

0.0595

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.0779

GnomAD4 exome

AF:

0.0910

AC:

91972

AN:

1011194

Hom.:

4398

AF XY:

0.0906

AC XY:

46184

AN XY:

509644

show subpopulations

African (AFR)

AF:

0.0175

AC:

410

AN:

23468

American (AMR)

AF:

0.0549

AC:

1702

AN:

31000

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

2168

AN:

19076

East Asian (EAS)

AF:

0.0121

AC:

426

AN:

35298

South Asian (SAS)

AF:

0.0447

AC:

2615

AN:

58498

European-Finnish (FIN)

AF:

0.0709

AC:

2799

AN:

39492

Middle Eastern (MID)

AF:

0.0937

AC:

435

AN:

4644

European-Non Finnish (NFE)

AF:

0.103

AC:

77768

AN:

755582

Other (OTH)

AF:

0.0827

AC:

3649

AN:

44136

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

3975

7949

11924

15898

19873

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2548

5096

7644

10192

12740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0669

AC:

10186

AN:

152186

Hom.:

447

Cov.:

AF XY:

0.0642

AC XY:

4778

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.0184

AC:

765

AN:

41534

American (AMR)

AF:

0.0633

AC:

967

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.120

AC:

418

AN:

3472

East Asian (EAS)

AF:

0.00733

AC:

AN:

5184

South Asian (SAS)

AF:

0.0405

AC:

195

AN:

4812

European-Finnish (FIN)

AF:

0.0595

AC:

630

AN:

10594

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6867

AN:

68002

Other (OTH)

AF:

0.0762

AC:

161

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

499

999

1498

1998

2497

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0822

Hom.:

108

Bravo

AF:

0.0644

Asia WGS

AF:

0.0350

AC:

122

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.2

(source)

DANN

Benign

0.32

PhyloP100

-0.99

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over