Variant chrX-12498658-C-CT 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.42-10dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0053 ( 4 hom., 118 hem., cov: 20)

Exomes 𝑓: 0.037 ( 0 hom. 19 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-C-CT is Benign according to our data. Variant chrX-12498658-C-CT is described in ClinVar as [Benign]. Clinvar id is 195297.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0531 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.42-10dup		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.42-10dup		intron_variant			NM_001368397.1	ENSP00000502607	P2

Frequencies

GnomAD3 genomes

AF:

0.00531

AC:

544

AN:

102364

Hom.:

Cov.:

AF XY:

0.00420

AC XY:

118

AN XY:

28098

show subpopulations

Gnomad AFR

AF:

0.0165

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00200

Gnomad ASJ

AF:

0.000399

Gnomad EAS

AF:

0.00301

Gnomad SAS

AF:

0.00565

Gnomad FIN

AF:

0.000725

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000501

Gnomad OTH

AF:

0.00371

GnomAD4 exome

AF:

0.0373

AC:

20479

AN:

549035

Hom.:

Cov.:

AF XY:

0.000132

AC XY:

AN XY:

143663

show subpopulations

Gnomad4 AFR exome

AF:

0.0564

Gnomad4 AMR exome

AF:

0.0415

Gnomad4 ASJ exome

AF:

0.0343

Gnomad4 EAS exome

AF:

0.0337

Gnomad4 SAS exome

AF:

0.0256

Gnomad4 FIN exome

AF:

0.0255

Gnomad4 NFE exome

AF:

0.0386

Gnomad4 OTH exome

AF:

0.0349

GnomAD4 genome

AF:

0.00532

AC:

544

AN:

102339

Hom.:

Cov.:

AF XY:

0.00420

AC XY:

118

AN XY:

28097

show subpopulations

Gnomad4 AFR

AF:

0.0165

Gnomad4 AMR

AF:

0.00199

Gnomad4 ASJ

AF:

0.000399

Gnomad4 EAS

AF:

0.00302

Gnomad4 SAS

AF:

0.00569

Gnomad4 FIN

AF:

0.000725

Gnomad4 NFE

AF:

0.000501

Gnomad4 OTH

AF:

0.00368

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)

Aug 08, 2014

- -

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