12-7062270-C-CAAAAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001734.5(C1S):​c.6-193_6-189dupAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 1980 hom., cov: 17)
Exomes 𝑓: 0.052 ( 8 hom. )
Failed GnomAD Quality Control

Consequence

C1S
NM_001734.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.29
Variant links:
Genes affected
C1S (HGNC:1247): (complement C1s) This gene encodes a serine protease, which is a major constituent of the human complement subcomponent C1. C1s associates with two other complement components C1r and C1q in order to yield the first component of the serum complement system. Defects in this gene are the cause of selective C1s deficiency. [provided by RefSeq, Mar 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 12-7062270-C-CAAAAA is Benign according to our data. Variant chr12-7062270-C-CAAAAA is described in ClinVar as [Benign]. Clinvar id is 1247086.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C1SNM_001734.5 linkc.6-193_6-189dupAAAAA intron_variant Intron 2 of 11 ENST00000360817.10 NP_001725.1 P09871
C1SNM_201442.4 linkc.6-193_6-189dupAAAAA intron_variant Intron 2 of 11 NP_958850.1 P09871
C1SNM_001346850.2 linkc.-289+365_-289+369dupAAAAA intron_variant Intron 2 of 10 NP_001333779.1 P09871F8WCZ6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C1SENST00000360817.10 linkc.6-205_6-204insAAAAA intron_variant Intron 2 of 11 1 NM_001734.5 ENSP00000354057.5 P09871

Frequencies

GnomAD3 genomes
AF:
0.161
AC:
17210
AN:
107172
Hom.:
1978
Cov.:
17
show subpopulations
Gnomad AFR
AF:
0.336
Gnomad AMI
AF:
0.0843
Gnomad AMR
AF:
0.106
Gnomad ASJ
AF:
0.125
Gnomad EAS
AF:
0.0679
Gnomad SAS
AF:
0.0890
Gnomad FIN
AF:
0.0587
Gnomad MID
AF:
0.163
Gnomad NFE
AF:
0.105
Gnomad OTH
AF:
0.151
GnomAD4 exome
AF:
0.0518
AC:
17007
AN:
328544
Hom.:
8
Cov.:
0
AF XY:
0.0516
AC XY:
9157
AN XY:
177624
show subpopulations
Gnomad4 AFR exome
AF:
0.183
Gnomad4 AMR exome
AF:
0.0509
Gnomad4 ASJ exome
AF:
0.0521
Gnomad4 EAS exome
AF:
0.0272
Gnomad4 SAS exome
AF:
0.0582
Gnomad4 FIN exome
AF:
0.0380
Gnomad4 NFE exome
AF:
0.0488
Gnomad4 OTH exome
AF:
0.0553
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.161
AC:
17213
AN:
107176
Hom.:
1980
Cov.:
17
AF XY:
0.158
AC XY:
7965
AN XY:
50394
show subpopulations
Gnomad4 AFR
AF:
0.336
Gnomad4 AMR
AF:
0.105
Gnomad4 ASJ
AF:
0.125
Gnomad4 EAS
AF:
0.0679
Gnomad4 SAS
AF:
0.0883
Gnomad4 FIN
AF:
0.0587
Gnomad4 NFE
AF:
0.105
Gnomad4 OTH
AF:
0.150

ClinVar

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

Submissions by phenotype

not provided Benign:1
Jun 19, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs373096669; hg19: chr12-7169574; API