Variant X-12706923-CTTTTTTTTT-CTTTTTTTT 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.1287+26delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 0 hom., 19 hem., cov: 10)

Exomes 𝑓: 0.17 ( 1 hom. 23 hem. )

Consequence

FRMPD4
NM_001368397.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.738

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:

FRMPD4 (HGNC:):

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-12706923-CT-C is Benign according to our data. Variant chrX-12706923-CT-C is described in ClinVar as [Benign]. Clinvar id is 402882.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-12706923-CT-C is described in Lovd as [Likely_benign].

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 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.1287+26delT		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.1287+26delT		intron_variant			NM_001368397.1	ENSP00000502607.1		A0A6Q8PH73

Frequencies

GnomAD3 genomes

AF:

0.00338

AC:

278

AN:

82262

Hom.:

Cov.:

AF XY:

0.00109

AC XY:

AN XY:

17442

show subpopulations

Gnomad AFR

AF:

0.00742

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00478

Gnomad ASJ

AF:

0.00142

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000646

Gnomad FIN

AF:

0.0120

Gnomad MID

AF:

0.00562

Gnomad NFE

AF:

0.00101

Gnomad OTH

AF:

0.00375

GnomAD3 exomes

AF:

0.200

AC:

10349

AN:

51637

Hom.:

AF XY:

0.00232

AC XY:

AN XY:

1293

show subpopulations

Gnomad AFR exome

AF:

0.216

Gnomad AMR exome

AF:

0.217

Gnomad ASJ exome

AF:

0.200

Gnomad EAS exome

AF:

0.233

Gnomad SAS exome

AF:

0.184

Gnomad FIN exome

AF:

0.118

Gnomad NFE exome

AF:

0.206

Gnomad OTH exome

AF:

0.195

GnomAD4 exome

AF:

0.169

AC:

75730

AN:

446898

Hom.:

Cov.:

AF XY:

0.000257

AC XY:

AN XY:

89548

show subpopulations

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.154

Gnomad4 ASJ exome

AF:

0.173

Gnomad4 EAS exome

AF:

0.205

Gnomad4 SAS exome

AF:

0.101

Gnomad4 FIN exome

AF:

0.141

Gnomad4 NFE exome

AF:

0.174

Gnomad4 OTH exome

AF:

0.185

GnomAD4 genome

AF:

0.00339

AC:

279

AN:

82247

Hom.:

Cov.:

AF XY:

0.00109

AC XY:

AN XY:

17437

show subpopulations

Gnomad4 AFR

AF:

0.00746

Gnomad4 AMR

AF:

0.00478

Gnomad4 ASJ

AF:

0.00142

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000651

Gnomad4 FIN

AF:

0.0120

Gnomad4 NFE

AF:

0.00101

Gnomad4 OTH

AF:

0.00371

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

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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