dbSNP rs4949402: SERINC2:p.Ile150Ile (chr1-31425387-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_178865.5(SERINC2):c.450T>C(p.Ile150Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 1,609,294 control chromosomes in the GnomAD database, including 234,734 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 0.45 ( 17229 hom., cov: 33)

Exomes 𝑓: 0.54 ( 217505 hom. )

Consequence

SERINC2
NM_178865.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.326

Publications

26 publications found

Variant links:

Genes affected

SERINC2 (HGNC:23231): (serine incorporator 2) Predicted to be involved in several processes, including phosphatidylserine metabolic process; positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity; and positive regulation of serine C-palmitoyltransferase activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

SERINC2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP7

Synonymous conserved (PhyloP=0.326 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) 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
SERINC2	NM_178865.5 link	c.450T>C	p.Ile150Ile	synonymous_variant	Exon 4 of 10	ENST00000373709.8	NP_849196.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERINC2	ENST00000373709.8 link	c.450T>C	p.Ile150Ile	synonymous_variant	Exon 4 of 10	1	NM_178865.5	ENSP00000362813.3

Frequencies

GnomAD3 genomes

AF:

0.447

AC:

67896

AN:

151854

Hom.:

17228

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.443

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.557

Gnomad EAS

AF:

0.343

Gnomad SAS

AF:

0.359

Gnomad FIN

AF:

0.529

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.575

Gnomad OTH

AF:

0.473

GnomAD2 exomes

AF:

0.491

AC:

123376

AN:

251328

AF XY:

0.495

show subpopulations

Gnomad AFR exome

AF:

0.209

Gnomad AMR exome

AF:

0.467

Gnomad ASJ exome

AF:

0.567

Gnomad EAS exome

AF:

0.349

Gnomad FIN exome

AF:

0.534

Gnomad NFE exome

AF:

0.579

Gnomad OTH exome

AF:

0.524

GnomAD4 exome

AF:

0.539

AC:

785556

AN:

1457322

Hom.:

217505

Cov.:

AF XY:

0.536

AC XY:

388456

AN XY:

725276

show subpopulations

African (AFR)

AF:

0.196

AC:

6552

AN:

33418

American (AMR)

AF:

0.469

AC:

20966

AN:

44710

Ashkenazi Jewish (ASJ)

AF:

0.562

AC:

14677

AN:

26118

East Asian (EAS)

AF:

0.310

AC:

12291

AN:

39680

South Asian (SAS)

AF:

0.373

AC:

32155

AN:

86172

European-Finnish (FIN)

AF:

0.536

AC:

28615

AN:

53368

Middle Eastern (MID)

AF:

0.519

AC:

2990

AN:

5756

European-Non Finnish (NFE)

AF:

0.574

AC:

636198

AN:

1107840

Other (OTH)

AF:

0.516

AC:

31112

AN:

60260

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

16454

32907

49361

65814

82268

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17188

34376

51564

68752

85940

<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:

0.447

AC:

67895

AN:

151972

Hom.:

17229

Cov.:

AF XY:

0.444

AC XY:

32985

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.212

AC:

8793

AN:

41436

American (AMR)

AF:

0.490

AC:

7482

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.557

AC:

1932

AN:

3468

East Asian (EAS)

AF:

0.344

AC:

1774

AN:

5158

South Asian (SAS)

AF:

0.358

AC:

1724

AN:

4820

European-Finnish (FIN)

AF:

0.529

AC:

5581

AN:

10542

Middle Eastern (MID)

AF:

0.520

AC:

153

AN:

294

European-Non Finnish (NFE)

AF:

0.575

AC:

39063

AN:

67956

Other (OTH)

AF:

0.470

AC:

991

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

1803

3607

5410

7214

9017

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

614

1228

1842

2456

3070

<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:

0.530

Hom.:

30115

Bravo

AF:

0.434

Asia WGS

AF:

0.319

AC:

1112

AN:

3478

EpiCase

AF:

0.582

EpiControl

AF:

0.581

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

0.33

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