Genetic Variant FRMPD4:c.1287+24_1287+26delTTT (chrX-12706923-CTTT-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001368397.1(FRMPD4):c.1287+24_1287+26delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00903 in 590,070 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000097 ( 0 hom., 0 hem., cov: 10)

Exomes 𝑓: 0.010 ( 0 hom. 0 hem. )

Consequence

FRMPD4
NM_001368397.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.48

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRMPD4	NM_001368397.1 link	c.1287+24_1287+26delTTT		intron_variant	Intron 12 of 16	ENST00000675598.1	NP_001355326.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRMPD4	ENST00000675598.1 link	c.1287+9_1287+11delTTT		intron_variant	Intron 12 of 16		NM_001368397.1	ENSP00000502607.1		A0A6Q8PH73

Frequencies

GnomAD3 genomes

AF:

0.0000972

AC:

AN:

82295

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

17461

show subpopulations

Gnomad AFR

AF:

0.0000447

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000422

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000461

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000705

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0172

AC:

889

AN:

51637

Hom.:

AF XY:

0.00

AC XY:

AN XY:

1293

show subpopulations

Gnomad AFR exome

AF:

0.0148

Gnomad AMR exome

AF:

0.0228

Gnomad ASJ exome

AF:

0.0196

Gnomad EAS exome

AF:

0.0237

Gnomad SAS exome

AF:

0.0206

Gnomad FIN exome

AF:

0.00502

Gnomad NFE exome

AF:

0.0166

Gnomad OTH exome

AF:

0.0199

GnomAD4 exome

AF:

0.0105

AC:

5319

AN:

507775

Hom.:

AF XY:

0.00

AC XY:

AN XY:

144515

show subpopulations

Gnomad4 AFR exome

AF:

0.0113

Gnomad4 AMR exome

AF:

0.0122

Gnomad4 ASJ exome

AF:

0.0117

Gnomad4 EAS exome

AF:

0.00845

Gnomad4 SAS exome

AF:

0.00858

Gnomad4 FIN exome

AF:

0.00580

Gnomad4 NFE exome

AF:

0.0111

Gnomad4 OTH exome

AF:

0.00937

GnomAD4 genome

AF:

0.0000972

AC:

AN:

82295

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

17461

show subpopulations

Gnomad4 AFR

AF:

0.0000447

Gnomad4 AMR

AF:

0.000422

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000461

Gnomad4 NFE

AF:

0.0000705

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

X-12706923-CTTTTTTTTT-CTTTTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over