chrX-12723383-T-G

Position:

• chrX-12723383-T-G

Variant summary

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

The NM_001368397.1(FRMPD4):​c.*1525T>G variant causes a 3 prime UTR 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 (16184 hom., 19782 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: FRMPD4 NM_001368397.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

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=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRMPD4	NM_001368397.1	c.*1525T>G		3_prime_UTR_variant	17/17	ENST00000675598.1	NP_001355326.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRMPD4	ENST00000675598.1	c.*1525T>G		3_prime_UTR_variant	17/17		NM_001368397.1	ENSP00000502607.1

Frequencies

GnomAD3 genomes AF: 0.633 AC: 69356 AN: 109550 Hom.: 16190 Cov.: 22 AF XY: 0.620 AC XY: 19745 AN XY: 31844

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.625

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.633 AC: 69378 AN: 109597 Hom.: 16184 Cov.: 22 AF XY: 0.620 AC XY: 19782 AN XY: 31901

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.623

Alfa AF: 0.618 Hom.: 5995

Bravo AF: 0.648

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.46

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: rs5979717; hg19: chrX-12741502;