chr6-75312516-C-G

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6

The NM_015687.5(FILIP1):​c.3316G>C​(p.Gly1106Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000477 in 1,614,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000036 ( 0 hom. )

Consequence

FILIP1
NM_015687.5 missense

Scores

4
8
7

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 6.17
Variant links:
Genes affected
FILIP1 (HGNC:21015): (filamin A interacting protein 1) This gene encodes a filamin A binding protein. The encoded protein promotes the degradation of filamin A and may regulate cortical neuron migration and dendritic spine morphology. Mice lacking a functional copy of this gene exhibit reduced dendritic spine length and altered excitatory signaling. [provided by RefSeq, Oct 2016]
TMEM30A-DT (HGNC:48985): (TMEM30A divergent transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.17751008).
BP6
Variant 6-75312516-C-G is Benign according to our data. Variant chr6-75312516-C-G is described in ClinVar as [Benign]. Clinvar id is 208956.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FILIP1NM_015687.5 linkuse as main transcriptc.3316G>C p.Gly1106Arg missense_variant 5/6 ENST00000237172.12 NP_056502.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FILIP1ENST00000237172.12 linkuse as main transcriptc.3316G>C p.Gly1106Arg missense_variant 5/61 NM_015687.5 ENSP00000237172 P4Q7Z7B0-1
TMEM30A-DTENST00000661161.1 linkuse as main transcriptn.445C>G non_coding_transcript_exon_variant 2/2

Frequencies

GnomAD3 genomes
AF:
0.000158
AC:
24
AN:
152116
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000875
AC:
22
AN:
251476
Hom.:
0
AF XY:
0.0000956
AC XY:
13
AN XY:
135914
show subpopulations
Gnomad AFR exome
AF:
0.000984
Gnomad AMR exome
AF:
0.0000289
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:
0.0000352
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.0000363
AC:
53
AN:
1461882
Hom.:
0
Cov.:
35
AF XY:
0.0000330
AC XY:
24
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.000299
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000297
Gnomad4 OTH exome
AF:
0.0000993
GnomAD4 genome
AF:
0.000158
AC:
24
AN:
152234
Hom.:
0
Cov.:
32
AF XY:
0.000175
AC XY:
13
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.000482
Gnomad4 AMR
AF:
0.0000653
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000208
Hom.:
0
Bravo
AF:
0.000189
ESP6500AA
AF:
0.000454
AC:
2
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000906
AC:
11
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Abnormality of neuronal migration Benign:1
Benign, no assertion criteria providedclinical testingGénétique et pathophysiologie de maladies neurodéveloppementales et épileptogènes, Institut de génétique et de biologie moléculaire et cellulaireOct 31, 2014- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.94
BayesDel_addAF
Benign
-0.059
T
BayesDel_noAF
Uncertain
0.090
CADD
Uncertain
24
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.15
.;T;T
Eigen
Uncertain
0.58
Eigen_PC
Uncertain
0.55
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Pathogenic
0.98
D;D;D
M_CAP
Benign
0.042
D
MetaRNN
Benign
0.18
T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.6
M;M;.
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Uncertain
0.67
T
PROVEAN
Uncertain
-3.2
D;D;D
REVEL
Benign
0.22
Sift
Uncertain
0.0030
D;D;D
Sift4G
Uncertain
0.0070
D;D;D
Polyphen
0.99
D;D;.
Vest4
0.54
MVP
0.81
MPC
0.78
ClinPred
0.28
T
GERP RS
5.0
Varity_R
0.37
gMVP
0.82

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

LitVar

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

Other links and lift over

dbSNP: rs374887916; hg19: chr6-76022232; API