NM_001352027.3:c.1685-15_1685-3delTTTTTTTTTTTTT

Variant names:

• chr11-45935741-TAAAAAAAAAAAAA-T
• rs35995547
• NM_001352027.3:c.1685-15_1685-3delTTTTTTTTTTTTT

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001352027.3(PHF21A):​c.1685-15_1685-3delTTTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000802 in 523,646 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.000083 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000079 (0 hom.)
• Consequence: PHF21A NM_001352027.3 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.62
• Publications: 2 publications found

Genes affected

PHF21A (HGNC:24156): (PHD finger protein 21A) The PHF21A gene encodes BHC80, a component of a BRAF35 (MIM 605535)/histone deacetylase (HDAC; see MIM 601241) complex (BHC) that mediates repression of neuron-specific genes through the cis-regulatory element known as repressor element-1 (RE1) or neural restrictive silencer (NRS) (Hakimi et al., 2002 [PubMed 12032298]).[supplied by OMIM, Nov 2010]

PHF21A Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• Potocki-Shaffer syndrome

  Inheritance: AD Classification: STRONG Submitted by: G2P

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP6: Variant 11-45935741-TAAAAAAAAAAAAA-T is Benign according to our data. Variant chr11-45935741-TAAAAAAAAAAAAA-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1979745.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 9 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF21A	NM_001352027.3	c.1685-15_1685-3delTTTTTTTTTTTTT		splice_region_variant, intron_variant	Intron 17 of 18	ENST00000676320.1	NP_001338956.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF21A	ENST00000676320.1	c.1685-15_1685-3delTTTTTTTTTTTTT		splice_region_variant, intron_variant	Intron 17 of 18		NM_001352027.3	ENSP00000502222.1

Frequencies

GnomAD3 genomes AF: 0.0000831 AC: 9 AN: 108338 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000291

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: 0.0000372

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000795 AC: 33 AN: 415308 Hom.: 0 AF XY: 0.0000547 AC XY: 12 AN XY: 219404

African (AFR) AF: 0.00 AC: 0 AN: 10636

American (AMR) AF: 0.0000591 AC: 1 AN: 16922

Ashkenazi Jewish (ASJ) AF: 0.0000833 AC: 1 AN: 12008

East Asian (EAS) AF: 0.00 AC: 0 AN: 25896

South Asian (SAS) AF: 0.00 AC: 0 AN: 39626

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26210

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2206

European-Non Finnish (NFE) AF: 0.000115 AC: 30 AN: 260194

Other (OTH) AF: 0.0000463 AC: 1 AN: 21610

GnomAD4 genome AF: 0.0000831 AC: 9 AN: 108338 Hom.: 0 Cov.: 0 AF XY: 0.0000997 AC XY: 5 AN XY: 50148

African (AFR) AF: 0.000140 AC: 4 AN: 28564

American (AMR) AF: 0.000291 AC: 3 AN: 10320

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2910

East Asian (EAS) AF: 0.00 AC: 0 AN: 3728

South Asian (SAS) AF: 0.00 AC: 0 AN: 3076

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3552

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 236

European-Non Finnish (NFE) AF: 0.0000372 AC: 2 AN: 53784

Other (OTH) AF: 0.00 AC: 0 AN: 1436

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 05, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs35995547; hg19: chr11-45957292;