X-132077924-G-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_194277.3(FRMD7):​c.2093C>A​(p.Pro698Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,096,615 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 23)
Exomes 𝑓: 0.000011 ( 0 hom. 3 hem. )

Consequence

FRMD7
NM_194277.3 missense

Scores

1
2
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.48
Variant links:
Genes affected
FRMD7 (HGNC:8079): (FERM domain containing 7) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of neuron projection development. Predicted to act upstream of or within several processes, including negative regulation of stress fiber assembly; positive regulation of lamellipodium assembly; and positive regulation of small GTPase mediated signal transduction. Located in cytosol; nucleoplasm; and plasma membrane. Implicated in congenital nystagmus 1. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.16585526).
BS2
High Hemizygotes in GnomAdExome4 at 3 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FRMD7NM_194277.3 linkc.2093C>A p.Pro698Gln missense_variant Exon 12 of 12 ENST00000298542.9 NP_919253.1 Q6ZUT3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FRMD7ENST00000298542.9 linkc.2093C>A p.Pro698Gln missense_variant Exon 12 of 12 1 NM_194277.3 ENSP00000298542.3 Q6ZUT3-1
FRMD7ENST00000464296.1 linkc.2048C>A p.Pro683Gln missense_variant Exon 12 of 12 1 ENSP00000417996.1 Q6ZUT3-2
FRMD7ENST00000370879.5 linkc.1733C>A p.Pro578Gln missense_variant Exon 8 of 8 1 ENSP00000359916.1 X6R7S7

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD3 exomes
AF:
0.00000547
AC:
1
AN:
182789
Hom.:
0
AF XY:
0.0000148
AC XY:
1
AN XY:
67495
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
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:
0.0000123
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000109
AC:
12
AN:
1096615
Hom.:
0
Cov.:
30
AF XY:
0.00000829
AC XY:
3
AN XY:
362029
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000143
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
23
ExAC
AF:
0.0000165
AC:
2

ClinVar

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

Submissions by phenotype

not provided Uncertain:1
Dec 31, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This sequence change replaces proline, which is neutral and non-polar, with glutamine, which is neutral and polar, at codon 698 of the FRMD7 protein (p.Pro698Gln). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with FRMD7-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.080
BayesDel_addAF
Benign
-0.072
T
BayesDel_noAF
Benign
-0.34
CADD
Benign
8.6
DANN
Benign
0.90
DEOGEN2
Benign
0.012
.;T;.
FATHMM_MKL
Benign
0.15
N
LIST_S2
Benign
0.52
T;T;T
M_CAP
Pathogenic
0.69
D
MetaRNN
Benign
0.17
T;T;T
MetaSVM
Benign
-0.62
T
MutationAssessor
Uncertain
2.0
.;M;.
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-0.29
N;N;N
REVEL
Benign
0.18
Sift
Uncertain
0.0010
D;D;D
Sift4G
Benign
0.15
T;T;T
Polyphen
0.090, 0.30
.;B;B
Vest4
0.091
MutPred
0.14
.;Loss of loop (P = 0.0128);.;
MVP
0.62
MPC
0.36
ClinPred
0.17
T
GERP RS
3.8
Varity_R
0.086
gMVP
0.12

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: rs755805433; hg19: chrX-131211952; API