chr5-39288709-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001737.5(C9):​c.1645+14A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00342 in 1,477,496 control chromosomes in the GnomAD database, including 155 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 101 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 54 hom. )

Consequence

C9
NM_001737.5 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.288
Variant links:
Genes affected
C9 (HGNC:1358): (complement C9) This gene encodes the final component of the complement system. It participates in the formation of the Membrane Attack Complex (MAC). The MAC assembles on bacterial membranes to form a pore, permitting disruption of bacterial membrane organization. Mutations in this gene cause component C9 deficiency. [provided by RefSeq, Feb 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 5-39288709-T-C is Benign according to our data. Variant chr5-39288709-T-C is described in ClinVar as [Benign]. Clinvar id is 1165576.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-39288709-T-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0607 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
C9NM_001737.5 linkuse as main transcriptc.1645+14A>G intron_variant ENST00000263408.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
C9ENST00000263408.5 linkuse as main transcriptc.1645+14A>G intron_variant 1 NM_001737.5 P2

Frequencies

GnomAD3 genomes
AF:
0.0179
AC:
2722
AN:
151862
Hom.:
101
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0629
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00527
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000177
Gnomad OTH
AF:
0.0134
GnomAD3 exomes
AF:
0.00473
AC:
1184
AN:
250126
Hom.:
32
AF XY:
0.00346
AC XY:
468
AN XY:
135228
show subpopulations
Gnomad AFR exome
AF:
0.0653
Gnomad AMR exome
AF:
0.00294
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000974
Gnomad OTH exome
AF:
0.00230
GnomAD4 exome
AF:
0.00176
AC:
2331
AN:
1325516
Hom.:
54
Cov.:
20
AF XY:
0.00151
AC XY:
1006
AN XY:
667166
show subpopulations
Gnomad4 AFR exome
AF:
0.0643
Gnomad4 AMR exome
AF:
0.00333
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000168
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000384
Gnomad4 OTH exome
AF:
0.00294
GnomAD4 genome
AF:
0.0179
AC:
2723
AN:
151980
Hom.:
101
Cov.:
32
AF XY:
0.0173
AC XY:
1284
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.0627
Gnomad4 AMR
AF:
0.00526
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000177
Gnomad4 OTH
AF:
0.0133
Alfa
AF:
0.0150
Hom.:
11
Bravo
AF:
0.0202
Asia WGS
AF:
0.00202
AC:
7
AN:
3476

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 21, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
3.3
DANN
Benign
0.52

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: rs700180; hg19: chr5-39288811; API