Variant X-12498658-CT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001368397.1(FRMPD4):c.42-10del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.025 ( 36 hom., 581 hem., cov: 20)

Exomes 𝑓: 0.14 ( 100 hom. 2023 hem. )

Consequence

FRMPD4
NM_001368397.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.927

Variant links:

Genes affected

FRMPD4 (HGNC:29007): (FERM and PDZ domain containing 4) This gene encodes a multi-domain (WW, PDZ, FERM) containing protein. Through its interaction with other proteins (such as PSD-95), it functions as a positive regulator of dendritic spine morphogenesis and density, and is required for the maintenance of excitatory synaptic transmission. [provided by RefSeq, Jan 2010]

FRMPD4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant X-12498658-CT-C is Benign according to our data. Variant chrX-12498658-CT-C is described in ClinVar as [Benign]. Clinvar id is 95617.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRMPD4	NM_001368397.1 linkuse as main transcript	c.42-10del		intron_variant		ENST00000675598.1	NP_001355326.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRMPD4	ENST00000675598.1 linkuse as main transcript	c.42-10del		intron_variant			NM_001368397.1	ENSP00000502607	P2

Frequencies

GnomAD3 genomes

AF:

0.0251

AC:

2563

AN:

102262

Hom.:

Cov.:

AF XY:

0.0207

AC XY:

581

AN XY:

28046

show subpopulations

Gnomad AFR

AF:

0.0146

Gnomad AMI

AF:

0.00152

Gnomad AMR

AF:

0.0142

Gnomad ASJ

AF:

0.0172

Gnomad EAS

AF:

0.00120

Gnomad SAS

AF:

0.00565

Gnomad FIN

AF:

0.0214

Gnomad MID

AF:

0.0132

Gnomad NFE

AF:

0.0366

Gnomad OTH

AF:

0.0268

GnomAD4 exome

AF:

0.137

AC:

61221

AN:

445980

Hom.:

100

Cov.:

AF XY:

0.0206

AC XY:

2023

AN XY:

98040

show subpopulations

Gnomad4 AFR exome

AF:

0.131

Gnomad4 AMR exome

AF:

0.165

Gnomad4 ASJ exome

AF:

0.146

Gnomad4 EAS exome

AF:

0.122

Gnomad4 SAS exome

AF:

0.0884

Gnomad4 FIN exome

AF:

0.147

Gnomad4 NFE exome

AF:

0.139

Gnomad4 OTH exome

AF:

0.145

GnomAD4 genome

AF:

0.0251

AC:

2563

AN:

102237

Hom.:

Cov.:

AF XY:

0.0207

AC XY:

581

AN XY:

28045

show subpopulations

Gnomad4 AFR

AF:

0.0146

Gnomad4 AMR

AF:

0.0142

Gnomad4 ASJ

AF:

0.0172

Gnomad4 EAS

AF:

0.00121

Gnomad4 SAS

AF:

0.00570

Gnomad4 FIN

AF:

0.0214

Gnomad4 NFE

AF:

0.0366

Gnomad4 OTH

AF:

0.0266

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

May 28, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over