X-12706923-CTTTTTTTTT-CTTTTTTTTTT

Position:

• chrX-12706923-CTTTTTTTTT-CTTTTTTTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001368397.1(FRMPD4):​c.1287+26dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.24 (2006 hom., 2707 hem., cov: 10)
  • Exomes 𝑓: 0.098 (43 hom. 222 hem.)
• Consequence: FRMPD4 NM_001368397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.738

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRMPD4	NM_001368397.1	c.1287+26dupT		intron_variant		ENST00000675598.1	NP_001355326.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRMPD4	ENST00000675598.1	c.1287+26dupT		intron_variant			NM_001368397.1	ENSP00000502607.1

Frequencies

GnomAD3 genomes AF: 0.238 AC: 19475 AN: 81941 Hom.: 2002 Cov.: 10 AF XY: 0.158 AC XY: 2704 AN XY: 17147

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.0526

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.235

GnomAD3 exomes AF: 0.0572 AC: 2955 AN: 51637 Hom.: 4 AF XY: 0.00619 AC XY: 8 AN XY: 1293

Gnomad AFR exome AF: 0.0610

Gnomad AMR exome AF: 0.0771

Gnomad ASJ exome AF: 0.0654

Gnomad EAS exome AF: 0.0405

Gnomad SAS exome AF: 0.0612

Gnomad FIN exome AF: 0.0534

Gnomad NFE exome AF: 0.0527

Gnomad OTH exome AF: 0.0646

GnomAD4 exome AF: 0.0977 AC: 47800 AN: 489004 Hom.: 43 Cov.: 0 AF XY: 0.00185 AC XY: 222 AN XY: 119990

Gnomad4 AFR exome AF: 0.103

Gnomad4 AMR exome AF: 0.0715

Gnomad4 ASJ exome AF: 0.0729

Gnomad4 EAS exome AF: 0.0335

Gnomad4 SAS exome AF: 0.0651

Gnomad4 FIN exome AF: 0.0961

Gnomad4 NFE exome AF: 0.107

Gnomad4 OTH exome AF: 0.0963

GnomAD4 genome AF: 0.238 AC: 19483 AN: 81926 Hom.: 2006 Cov.: 10 AF XY: 0.158 AC XY: 2707 AN XY: 17142

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.0533

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs746601138; hg19: chrX-12725042;