Genetic Variant PHF21A:c.1685-12_1685-3delTTTTTTTTTT (chr11-45935741-TAAAAAAAAAA-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001352027.3(PHF21A):c.1685-12_1685-3delTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000169 in 415,278 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000017 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

PHF21A
NM_001352027.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.62

Publications

0 publications found

Variant links:

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

PHF21A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352027.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PHF21A	NM_001352027.3	MANE Select	c.1685-12_1685-3delTTTTTTTTTT	splice_region intron	N/A	NP_001338956.1
PHF21A	NM_001441167.1		c.1706-12_1706-3delTTTTTTTTTT	splice_region intron	N/A	NP_001428096.1
PHF21A	NM_001441168.1		c.1706-12_1706-3delTTTTTTTTTT	splice_region intron	N/A	NP_001428097.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PHF21A	ENST00000676320.1	MANE Select	c.1685-12_1685-3delTTTTTTTTTT	splice_region intron	N/A	ENSP00000502222.1
PHF21A	ENST00000323180.10	TSL:1	c.1544-12_1544-3delTTTTTTTTTT	splice_region intron	N/A	ENSP00000323152.6
PHF21A	ENST00000418153.6	TSL:2	c.1682-12_1682-3delTTTTTTTTTT	splice_region intron	N/A	ENSP00000398824.2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

108336

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

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:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000169

AC:

AN:

415278

Hom.:

AF XY:

0.0000182

AC XY:

AN XY:

219386

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

10634

American (AMR)

AF:

0.00

AC:

AN:

16920

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12004

East Asian (EAS)

AF:

0.00

AC:

AN:

25896

South Asian (SAS)

AF:

0.0000252

AC:

AN:

39624

European-Finnish (FIN)

AF:

0.00

AC:

AN:

26206

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2206

European-Non Finnish (NFE)

AF:

0.0000231

AC:

AN:

260182

Other (OTH)

AF:

0.00

AC:

AN:

21606

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.246

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

108336

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

50148

African (AFR)

AF:

0.00

AC:

AN:

28564

American (AMR)

AF:

0.00

AC:

AN:

10320

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2910

East Asian (EAS)

AF:

0.00

AC:

AN:

3728

South Asian (SAS)

AF:

0.00

AC:

AN:

3074

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3552

Middle Eastern (MID)

AF:

0.00

AC:

AN:

236

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

53784

Other (OTH)

AF:

0.00

AC:

AN:

1436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.6

Splicing

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

Publications

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11-45935741-TAAAAAAAAAAAAAA-TAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over