X-12498658-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.927

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]

ACMG classification

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	UniProt
FRMPD4	NM_001368397.1	c.42-10del		intron_variant		ENST00000675598.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0251 AC: 2563 AN: 102262 Hom.: 36 Cov.: 20 AF XY: 0.0207 AC XY: 581 AN XY: 28046

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.: 0 AF XY: 0.0206 AC XY: 2023 AN XY: 98040

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.: 36 Cov.: 20 AF XY: 0.0207 AC XY: 581 AN XY: 28045

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

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

May 28, 2013

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Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs111618469; hg19: chrX-12516777;