dbSNP rs2275435: SERINC2:c.473-87C>T (chr1-31425689-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_178865.5(SERINC2):c.473-87C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 1,470,186 control chromosomes in the GnomAD database, including 211,129 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 0.44 ( 16945 hom., cov: 33)

Exomes 𝑓: 0.53 ( 194184 hom. )

Consequence

SERINC2
NM_178865.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.394

Publications

11 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:

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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178865.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SERINC2	NM_178865.5	MANE Select	c.473-87C>T	intron	N/A	NP_849196.2	Q96SA4-1
SERINC2	NM_001199038.2		c.500-87C>T	intron	N/A	NP_001185967.1	Q96SA4-4
SERINC2	NM_001199037.2		c.485-87C>T	intron	N/A	NP_001185966.1	Q96SA4-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SERINC2	ENST00000373709.8	TSL:1 MANE Select	c.473-87C>T	intron	N/A	ENSP00000362813.3	Q96SA4-1
SERINC2	ENST00000851492.1		c.473-87C>T	intron	N/A	ENSP00000521551.1
SERINC2	ENST00000851493.1		c.473-87C>T	intron	N/A	ENSP00000521552.1

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

66941

AN:

151918

Hom.:

16944

Cov.:

show subpopulations

Gnomad AFR

AF:

0.211

Gnomad AMI

AF:

0.443

Gnomad AMR

AF:

0.487

Gnomad ASJ

AF:

0.557

Gnomad EAS

AF:

0.204

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.529

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.468

GnomAD4 exome

AF:

0.533

AC:

702842

AN:

1318150

Hom.:

194184

AF XY:

0.530

AC XY:

346747

AN XY:

654458

show subpopulations

African (AFR)

AF:

0.195

AC:

6028

AN:

30864

American (AMR)

AF:

0.462

AC:

18626

AN:

40300

Ashkenazi Jewish (ASJ)

AF:

0.561

AC:

12455

AN:

22182

East Asian (EAS)

AF:

0.183

AC:

7107

AN:

38832

South Asian (SAS)

AF:

0.364

AC:

27300

AN:

74998

European-Finnish (FIN)

AF:

0.538

AC:

25274

AN:

46982

Middle Eastern (MID)

AF:

0.510

AC:

1912

AN:

3750

European-Non Finnish (NFE)

AF:

0.573

AC:

576235

AN:

1005192

Other (OTH)

AF:

0.507

AC:

27905

AN:

55050

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

15843

31687

47530

63374

79217

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15420

30840

46260

61680

77100

<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:

0.440

AC:

66942

AN:

152036

Hom.:

16945

Cov.:

AF XY:

0.437

AC XY:

32471

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.210

AC:

8719

AN:

41454

American (AMR)

AF:

0.487

AC:

7435

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.557

AC:

1929

AN:

3464

East Asian (EAS)

AF:

0.204

AC:

1052

AN:

5164

South Asian (SAS)

AF:

0.347

AC:

1678

AN:

4832

European-Finnish (FIN)

AF:

0.529

AC:

5601

AN:

10584

Middle Eastern (MID)

AF:

0.517

AC:

151

AN:

292

European-Non Finnish (NFE)

AF:

0.574

AC:

38994

AN:

67948

Other (OTH)

AF:

0.465

AC:

980

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1788

3575

5363

7150

8938

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

602

1204

1806

2408

3010

<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:

0.501

Hom.:

3118

Bravo

AF:

0.427

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.6

(source)

DANN

Benign

0.62

PhyloP100

-0.39

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over