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GeneBe

6-109693679-C-T

Variant summary

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

The NM_014845.6(FIG4):c.66+2178C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,074 control chromosomes in the GnomAD database, including 47,486 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 0.79 ( 47486 hom., cov: 30)

Consequence

FIG4
NM_014845.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.60
Variant links:
Genes affected
FIG4 (HGNC:16873): (FIG4 phosphoinositide 5-phosphatase) The protein encoded by this gene belongs to the SAC domain-containing protein gene family. The SAC domain, approximately 400 amino acids in length and consisting of seven conserved motifs, has been shown to possess phosphoinositide phosphatase activity. The yeast homolog, Sac1p, is involved in the regulation of various phosphoinositides, and affects diverse cellular functions such as actin cytoskeleton organization, Golgi function, and maintenance of vacuole morphology. Membrane-bound phosphoinositides function as signaling molecules and play a key role in vesicle trafficking in eukaryotic cells. Mutations in this gene have been associated with Charcot-Marie-Tooth disease, type 4J. [provided by RefSeq, Jul 2008]

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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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FIG4NM_014845.6 linkuse as main transcriptc.66+2178C>T intron_variant ENST00000230124.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FIG4ENST00000230124.8 linkuse as main transcriptc.66+2178C>T intron_variant 1 NM_014845.6 P4

Frequencies

GnomAD3 genomes
AF:
0.789
AC:
119875
AN:
151956
Hom.:
47440
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.865
Gnomad AMI
AF:
0.703
Gnomad AMR
AF:
0.764
Gnomad ASJ
AF:
0.766
Gnomad EAS
AF:
0.687
Gnomad SAS
AF:
0.665
Gnomad FIN
AF:
0.783
Gnomad MID
AF:
0.750
Gnomad NFE
AF:
0.769
Gnomad OTH
AF:
0.775
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.789
AC:
119985
AN:
152074
Hom.:
47486
Cov.:
30
AF XY:
0.786
AC XY:
58415
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.865
Gnomad4 AMR
AF:
0.764
Gnomad4 ASJ
AF:
0.766
Gnomad4 EAS
AF:
0.688
Gnomad4 SAS
AF:
0.665
Gnomad4 FIN
AF:
0.783
Gnomad4 NFE
AF:
0.769
Gnomad4 OTH
AF:
0.774
Alfa
AF:
0.754
Hom.:
4030
Bravo
AF:
0.792
Asia WGS
AF:
0.696
AC:
2425
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
Cadd
Benign
0.094
Dann
Benign
0.34

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: rs829811; hg19: chr6-110014882; API