X-11864438-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001368395.3(FRMPD4):c.-103-648C>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 0.63 (15335 hom., 19341 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: FRMPD4 NM_001368395.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS2: High Homozygotes in GnomAd at 15345 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FRMPD4	NM_001368395.3	c.-103-648C>T		intron_variant
FRMPD4	NM_001368398.3	c.-103-648C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FRMPD4	ENST00000640291.2	c.-160-648C>T		intron_variant		5		A2
FRMPD4	ENST00000656302.1	c.-160-648C>T		intron_variant
FRMPD4	ENST00000673271.2	n.275-648C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.629 AC: 67951 AN: 108044 Hom.: 15345 Cov.: 21 AF XY: 0.634 AC XY: 19299 AN XY: 30448

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.650

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: 0.629 AC: 67976 AN: 108099 Hom.: 15335 Cov.: 21 AF XY: 0.634 AC XY: 19341 AN XY: 30513

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.645

Alfa AF: 0.628 Hom.: 8064

Bravo AF: 0.629

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.32
Dann	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1534285; hg19: chrX-11882557;