dbSNP rs3790557: SERBP1:c.951+295C>G (chr1-67419714-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_001018069.2(SERBP1):c.951+295C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00592 in 288,510 control chromosomes in the GnomAD database, including 25 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 0.0059 ( 13 hom., cov: 32)

Exomes 𝑓: 0.0060 ( 12 hom. )

Consequence

SERBP1
NM_001018069.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.10

Publications

1 publications found

Variant links:

Genes affected

SERBP1 (HGNC:17860): (SERPINE1 mRNA binding protein 1) Enables SUMO binding activity; mRNA 3'-UTR binding activity; and ribosome binding activity. Involved in PML body organization. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SERBP1 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=-0.87).

BS1

Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00589 (896/152164) while in subpopulation EAS AF = 0.0437 (226/5176). AF 95% confidence interval is 0.039. There are 13 homozygotes in GnomAd4. There are 440 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High AC in GnomAd4 at 896 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SERBP1	NM_001018069.2 link	c.951+295C>G	intron_variant	Intron 6 of 7	ENST00000361219.11	NP_001018079.1	Q8NC51-3
SERBP1	NM_001018067.2 link	c.996+295C>G	intron_variant	Intron 6 of 7		NP_001018077.1	Q8NC51-1
SERBP1	NM_001018068.2 link	c.978+295C>G	intron_variant	Intron 6 of 7		NP_001018078.1	Q8NC51-2
SERBP1	NM_015640.4 link	c.933+295C>G	intron_variant	Intron 6 of 7		NP_056455.3	Q8NC51-4Q5VU21Q63HR1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERBP1	ENST00000361219.11 link	c.951+295C>G		intron_variant	Intron 6 of 7	1	NM_001018069.2	ENSP00000354591.6		Q8NC51-3

Frequencies

GnomAD3 genomes

AF:

0.00588

AC:

894

AN:

152046

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000918

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0126

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.0434

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00727

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00497

Gnomad OTH

AF:

0.00526

GnomAD4 exome

AF:

0.00596

AC:

812

AN:

136346

Hom.:

AF XY:

0.00547

AC XY:

395

AN XY:

72254

show subpopulations

African (AFR)

AF:

0.00134

AC:

AN:

2992

American (AMR)

AF:

0.0147

AC:

AN:

5036

Ashkenazi Jewish (ASJ)

AF:

0.00165

AC:

AN:

4240

East Asian (EAS)

AF:

0.0418

AC:

256

AN:

6124

South Asian (SAS)

AF:

0.000724

AC:

AN:

15192

European-Finnish (FIN)

AF:

0.00576

AC:

AN:

6594

Middle Eastern (MID)

AF:

0.00327

AC:

AN:

612

European-Non Finnish (NFE)

AF:

0.00399

AC:

349

AN:

87386

Other (OTH)

AF:

0.00869

AC:

AN:

8170

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

118

157

196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.00589

AC:

896

AN:

152164

Hom.:

Cov.:

AF XY:

0.00591

AC XY:

440

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.000915

AC:

AN:

41524

American (AMR)

AF:

0.0126

AC:

192

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.000576

AC:

AN:

3472

East Asian (EAS)

AF:

0.0437

AC:

226

AN:

5176

South Asian (SAS)

AF:

0.000622

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00727

AC:

AN:

10586

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00497

AC:

338

AN:

67988

Other (OTH)

AF:

0.00568

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

143

191

239

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00842

Hom.:

Bravo

AF:

0.00605

Asia WGS

AF:

0.0310

AC:

108

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.56

(source)

DANN

Benign

0.57

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism

(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