X-12182662-C-T

Position:

• chrX-12182662-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001368397.1(FRMPD4):​c.41+43650C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.78 (24128 hom., 24200 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: FRMPD4 NM_001368397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRMPD4	NM_001368397.1	c.41+43650C>T		intron_variant		ENST00000675598.1	NP_001355326.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRMPD4	ENST00000675598.1	c.41+43650C>T		intron_variant			NM_001368397.1	ENSP00000502607.1

Frequencies

GnomAD3 genomes AF: 0.783 AC: 84895 AN: 108420 Hom.: 24127 Cov.: 21 AF XY: 0.784 AC XY: 24166 AN XY: 30826

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.766

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.783 AC: 84932 AN: 108455 Hom.: 24128 Cov.: 21 AF XY: 0.784 AC XY: 24200 AN XY: 30871

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.769

Alfa AF: 0.726 Hom.: 83707

Bravo AF: 0.799

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.67

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: rs6530488; hg19: chrX-12200781;