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GeneBe

18-63902544-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_002575.3(SERPINB2):c.819C>T(p.Ala273=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00032 in 1,613,136 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00034 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00032 ( 2 hom. )

Consequence

SERPINB2
NM_002575.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.36
Variant links:
Genes affected
SERPINB2 (HGNC:8584): (serpin family B member 2) Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to be involved in negative regulation of endopeptidase activity. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 18-63902544-C-T is Benign according to our data. Variant chr18-63902544-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 747521.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.36 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SERPINB2NM_002575.3 linkuse as main transcriptc.819C>T p.Ala273= synonymous_variant 7/8 ENST00000299502.9
SERPINB2NM_001143818.2 linkuse as main transcriptc.819C>T p.Ala273= synonymous_variant 8/9
SERPINB2XM_024451192.2 linkuse as main transcriptc.819C>T p.Ala273= synonymous_variant 7/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SERPINB2ENST00000299502.9 linkuse as main transcriptc.819C>T p.Ala273= synonymous_variant 7/81 NM_002575.3 P1
SERPINB2ENST00000457692.5 linkuse as main transcriptc.819C>T p.Ala273= synonymous_variant 8/95 P1
SERPINB2ENST00000482254.1 linkuse as main transcriptn.775C>T non_coding_transcript_exon_variant 6/65

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000335
AC:
51
AN:
152120
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00138
Gnomad ASJ
AF:
0.00202
Gnomad EAS
AF:
0.000579
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000221
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000498
AC:
124
AN:
249246
Hom.:
0
AF XY:
0.000445
AC XY:
60
AN XY:
134788
show subpopulations
Gnomad AFR exome
AF:
0.000124
Gnomad AMR exome
AF:
0.00120
Gnomad ASJ exome
AF:
0.00110
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000625
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000398
Gnomad OTH exome
AF:
0.000989
GnomAD4 exome
AF:
0.000319
AC:
466
AN:
1460898
Hom.:
2
Cov.:
31
AF XY:
0.000330
AC XY:
240
AN XY:
726734
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.00116
Gnomad4 ASJ exome
AF:
0.00123
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000661
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.000247
Gnomad4 OTH exome
AF:
0.000680
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000335
AC:
51
AN:
152238
Hom.:
0
Cov.:
32
AF XY:
0.000363
AC XY:
27
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.0000481
Gnomad4 AMR
AF:
0.00137
Gnomad4 ASJ
AF:
0.00202
Gnomad4 EAS
AF:
0.000580
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000221
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000507
Hom.:
0
Bravo
AF:
0.000453
Asia WGS
AF:
0.00375
AC:
13
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
Cadd
Benign
1.6
Dann
Benign
0.76

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs147312209; hg19: chr18-61569778; COSMIC: COSV55091682; COSMIC: COSV55091682; API