6-75428844-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015687.5(FILIP1):​c.-6-13866T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 150,496 control chromosomes in the GnomAD database, including 37,363 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 0.70 ( 37363 hom., cov: 31)

Consequence

FILIP1
NM_015687.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.65
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FILIP1NM_015687.5 linkuse as main transcriptc.-6-13866T>C intron_variant ENST00000237172.12
LOC101928540NR_125859.1 linkuse as main transcriptn.208+13648A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FILIP1ENST00000237172.12 linkuse as main transcriptc.-6-13866T>C intron_variant 1 NM_015687.5 P4Q7Z7B0-1
FILIP1ENST00000393004.6 linkuse as main transcriptc.-6-13866T>C intron_variant 1 A1Q7Z7B0-2

Frequencies

GnomAD3 genomes
AF:
0.697
AC:
104844
AN:
150402
Hom.:
37338
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.854
Gnomad AMI
AF:
0.573
Gnomad AMR
AF:
0.566
Gnomad ASJ
AF:
0.629
Gnomad EAS
AF:
0.584
Gnomad SAS
AF:
0.709
Gnomad FIN
AF:
0.597
Gnomad MID
AF:
0.720
Gnomad NFE
AF:
0.663
Gnomad OTH
AF:
0.666
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.697
AC:
104900
AN:
150496
Hom.:
37363
Cov.:
31
AF XY:
0.692
AC XY:
50977
AN XY:
73620
show subpopulations
Gnomad4 AFR
AF:
0.854
Gnomad4 AMR
AF:
0.565
Gnomad4 ASJ
AF:
0.629
Gnomad4 EAS
AF:
0.584
Gnomad4 SAS
AF:
0.709
Gnomad4 FIN
AF:
0.597
Gnomad4 NFE
AF:
0.663
Gnomad4 OTH
AF:
0.659
Alfa
AF:
0.587
Hom.:
1854
Bravo
AF:
0.700
Asia WGS
AF:
0.627
AC:
2177
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.040
DANN
Benign
0.56

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: rs2951929; hg19: chr6-76138560; API