X-134393642-T-C

Position:

• chrX-134393642-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001015877.2(PHF6):​c.374+8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00231 in 1,192,374 control chromosomes in the GnomAD database, including 83 homozygotes. There are 729 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0036 (5 hom., 131 hem., cov: 23)
  • Exomes 𝑓: 0.0022 (78 hom. 598 hem.)
• Consequence: PHF6 NM_001015877.2 splice_region, intron
• Scores: Splicing: ADA: 0.0005090
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: 0.0270

Genes affected

PHF6 (HGNC:18145): (PHD finger protein 6) This gene is a member of the plant homeodomain (PHD)-like finger (PHF) family. It encodes a protein with two PHD-type zinc finger domains, indicating a potential role in transcriptional regulation, that localizes to the nucleolus. Mutations affecting the coding region of this gene or the splicing of the transcript have been associated with Borjeson-Forssman-Lehmann syndrome (BFLS), a disorder characterized by cognitive disability, epilepsy, hypogonadism, hypometabolism, obesity, swelling of subcutaneous tissue of the face, narrow palpebral fissures, and large ears. Alternate splicing results in multiple transcript variants, encoding different isoforms. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BP6: Variant X-134393642-T-C is Benign according to our data. Variant chrX-134393642-T-C is described in ClinVar as [Benign]. Clinvar id is 96221.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF6	NM_001015877.2	c.374+8T>C		splice_region_variant, intron_variant		ENST00000370803.8	NP_001015877.1
PHF6	NM_032335.3	c.374+8T>C		splice_region_variant, intron_variant			NP_115711.2
PHF6	NM_032458.3	c.374+8T>C		splice_region_variant, intron_variant			NP_115834.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHF6	ENST00000370803.8	c.374+8T>C		splice_region_variant, intron_variant		1	NM_001015877.2	ENSP00000359839	P4

Frequencies

GnomAD3 genomes AF: 0.00364 AC: 407 AN: 111781 Hom.: 6 Cov.: 23 AF XY: 0.00380 AC XY: 129 AN XY: 33969

Gnomad AFR AF: 0.000453

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000113

Gnomad OTH AF: 0.00468

GnomAD3 exomes AF: 0.0103 AC: 1789 AN: 173050 Hom.: 69 AF XY: 0.00628 AC XY: 372 AN XY: 59266

Gnomad AFR exome AF: 0.000390

Gnomad AMR exome AF: 0.0674

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000258

Gnomad OTH exome AF: 0.00811

GnomAD4 exome AF: 0.00217 AC: 2350 AN: 1080547 Hom.: 78 Cov.: 27 AF XY: 0.00172 AC XY: 598 AN XY: 347697

Gnomad4 AFR exome AF: 0.000384

Gnomad4 AMR exome AF: 0.0650

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000229

Gnomad4 OTH exome AF: 0.00215

GnomAD4 genome AF: 0.00362 AC: 405 AN: 111827 Hom.: 5 Cov.: 23 AF XY: 0.00385 AC XY: 131 AN XY: 34025

Gnomad4 AFR AF: 0.000452

Gnomad4 AMR AF: 0.0359

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000113

Gnomad4 OTH AF: 0.00462

Alfa AF: 0.00219 Hom.: 7

Bravo AF: 0.00752

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Aug 12, 2013	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Apr 07, 2014	- -

Borjeson-Forssman-Lehmann syndrome Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Sep 13, 2023	- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	8.2
DANN	Benign	0.90

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00051
dbscSNV1_RF	Benign	0.40
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: rs142596708; hg19: chrX-133527672;