rs2407843

Positions:

• chrX-12425940-G-A
• chrX-12425940-G-C
• chrX-12425940-G-T

Variant summary

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

The NM_001368397.1(FRMPD4):​c.42-72740G>A 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 0.61 (15050 hom., 19927 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: FRMPD4 NM_001368397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRMPD4	NM_001368397.1	c.42-72740G>A		intron_variant		ENST00000675598.1	NP_001355326.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRMPD4	ENST00000675598.1	c.42-72740G>A		intron_variant			NM_001368397.1	ENSP00000502607	P2

Frequencies

GnomAD3 genomes AF: 0.610 AC: 67403 AN: 110450 Hom.: 15054 Cov.: 22 AF XY: 0.608 AC XY: 19887 AN XY: 32694

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.629

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: 0.610 AC: 67431 AN: 110507 Hom.: 15050 Cov.: 22 AF XY: 0.608 AC XY: 19927 AN XY: 32759

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.634

Alfa AF: 0.667 Hom.: 47889

Bravo AF: 0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.59
DANN	Benign	0.64

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: rs2407843; hg19: chrX-12444059;