Genetic Variant NM_003005.4:c.2102-15A>C (chr1-169594892-T-G) – 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.2102-15A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 1,602,256 control chromosomes in the GnomAD database, including 45,010 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 0.30 ( 9168 hom., cov: 33)

Exomes 𝑓: 0.21 ( 35842 hom. )

Consequence

SELP
NM_003005.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.322

Publications

11 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELP	NM_003005.4 link	c.2102-15A>C		intron_variant	Intron 12 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.2102-15A>C		intron_variant	Intron 12 of 16	1	NM_003005.4	ENSP00000263686.5		P16109

Frequencies

GnomAD3 genomes

AF:

0.297

AC:

45133

AN:

152012

Hom.:

9153

Cov.:

show subpopulations

Gnomad AFR

AF:

0.576

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.206

Gnomad EAS

AF:

0.00829

Gnomad SAS

AF:

0.0745

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.245

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.280

GnomAD2 exomes

AF:

0.190

AC:

47024

AN:

247080

AF XY:

0.182

show subpopulations

Gnomad AFR exome

AF:

0.589

Gnomad AMR exome

AF:

0.145

Gnomad ASJ exome

AF:

0.201

Gnomad EAS exome

AF:

0.00855

Gnomad FIN exome

AF:

0.144

Gnomad NFE exome

AF:

0.213

Gnomad OTH exome

AF:

0.205

GnomAD4 exome

AF:

0.207

AC:

300204

AN:

1450124

Hom.:

35842

Cov.:

AF XY:

0.202

AC XY:

145672

AN XY:

720114

show subpopulations

African (AFR)

AF:

0.591

AC:

19579

AN:

33150

American (AMR)

AF:

0.154

AC:

6768

AN:

44024

Ashkenazi Jewish (ASJ)

AF:

0.204

AC:

5273

AN:

25852

East Asian (EAS)

AF:

0.0118

AC:

468

AN:

39516

South Asian (SAS)

AF:

0.0781

AC:

6665

AN:

85386

European-Finnish (FIN)

AF:

0.150

AC:

7978

AN:

53184

Middle Eastern (MID)

AF:

0.219

AC:

1247

AN:

5700

European-Non Finnish (NFE)

AF:

0.217

AC:

239175

AN:

1103508

Other (OTH)

AF:

0.218

AC:

13051

AN:

59804

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

10913

21826

32739

43652

54565

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.297

AC:

45189

AN:

152132

Hom.:

9168

Cov.:

AF XY:

0.286

AC XY:

21271

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.576

AC:

23903

AN:

41480

American (AMR)

AF:

0.207

AC:

3167

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.206

AC:

715

AN:

3468

East Asian (EAS)

AF:

0.00830

AC:

AN:

5178

South Asian (SAS)

AF:

0.0746

AC:

360

AN:

4826

European-Finnish (FIN)

AF:

0.137

AC:

1450

AN:

10606

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.217

AC:

14779

AN:

67986

Other (OTH)

AF:

0.279

AC:

588

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1440

2880

4321

5761

7201

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.250

Hom.:

2826

Bravo

AF:

0.317

Asia WGS

AF:

0.0930

AC:

328

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.7

(source)

DANN

Benign

0.70

PhyloP100

-0.32

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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NM_003005.4:c.2102-15A>C

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