X-12498658-C-CT

Variant summary

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

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
• 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-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	UniProt
FRMPD4	NM_001368397.1	c.42-10dup		intron_variant		ENST00000675598.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00531 AC: 544 AN: 102364 Hom.: 4 Cov.: 20 AF XY: 0.00420 AC XY: 118 AN XY: 28098

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.: 0 Cov.: 0 AF XY: 0.000132 AC XY: 19 AN XY: 143663

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.: 4 Cov.: 20 AF XY: 0.00420 AC XY: 118 AN XY: 28097

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

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

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;