chrX-12706923-C-CTT

Position:

• chrX-12706923-C-CTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001368397.1(FRMPD4):​c.1287+25_1287+26dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.022 (48 hom., 192 hem., cov: 10)
  • Exomes 𝑓: 0.0077 (1 hom. 10 hem.)
• Consequence: FRMPD4 NM_001368397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.738

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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRMPD4	NM_001368397.1	c.1287+25_1287+26dupTT		intron_variant		ENST00000675598.1	NP_001355326.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRMPD4	ENST00000675598.1	c.1287+25_1287+26dupTT		intron_variant			NM_001368397.1	ENSP00000502607.1

Frequencies

GnomAD3 genomes AF: 0.0218 AC: 1795 AN: 82185 Hom.: 48 Cov.: 10 AF XY: 0.0111 AC XY: 193 AN XY: 17403

Gnomad AFR AF: 0.0615

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0390

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.000647

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00562

Gnomad NFE AF: 0.00101

Gnomad OTH AF: 0.0243

GnomAD3 exomes AF: 0.00924 AC: 477 AN: 51637 Hom.: 2 AF XY: 0.00155 AC XY: 2 AN XY: 1293

Gnomad AFR exome AF: 0.0160

Gnomad AMR exome AF: 0.0181

Gnomad ASJ exome AF: 0.00622

Gnomad EAS exome AF: 0.0122

Gnomad SAS exome AF: 0.00606

Gnomad FIN exome AF: 0.00502

Gnomad NFE exome AF: 0.00633

Gnomad OTH exome AF: 0.00746

GnomAD4 exome AF: 0.00770 AC: 4005 AN: 520195 Hom.: 1 Cov.: 0 AF XY: 0.0000668 AC XY: 10 AN XY: 149597

Gnomad4 AFR exome AF: 0.0240

Gnomad4 AMR exome AF: 0.0159

Gnomad4 ASJ exome AF: 0.00507

Gnomad4 EAS exome AF: 0.0146

Gnomad4 SAS exome AF: 0.00433

Gnomad4 FIN exome AF: 0.00495

Gnomad4 NFE exome AF: 0.00677

Gnomad4 OTH exome AF: 0.00840

GnomAD4 genome AF: 0.0218 AC: 1795 AN: 82169 Hom.: 48 Cov.: 10 AF XY: 0.0110 AC XY: 192 AN XY: 17397

Gnomad4 AFR AF: 0.0614

Gnomad4 AMR AF: 0.0391

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0288

Gnomad4 SAS AF: 0.000651

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00101

Gnomad4 OTH AF: 0.0241

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs746601138; hg19: chrX-12725042;