22-44888043-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_138415.5(PHF21B):​c.1117G>A​(p.Ala373Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000057 in 1,403,862 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000057 ( 0 hom. )

Consequence

PHF21B
NM_138415.5 missense

Scores

1
8
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.63
Variant links:
Genes affected
PHF21B (HGNC:25161): (PHD finger protein 21B) Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PHF21BNM_138415.5 linkc.1117G>A p.Ala373Thr missense_variant 10/13 ENST00000313237.10 NP_612424.1 Q96EK2-1A0A0S2Z6R3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PHF21BENST00000313237.10 linkc.1117G>A p.Ala373Thr missense_variant 10/131 NM_138415.5 ENSP00000324403.5 Q96EK2-1
PHF21BENST00000629843.3 linkc.991G>A p.Ala331Thr missense_variant 10/131 ENSP00000487086.1 Q96EK2-3
PHF21BENST00000396103.7 linkc.955G>A p.Ala319Thr missense_variant 10/132 Q96EK2-4
PHF21BENST00000403565.5 linkc.505G>A p.Ala169Thr missense_variant 11/142 ENSP00000385053.2 B1AHC5

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.0000187
AC:
3
AN:
160782
Hom.:
0
AF XY:
0.0000351
AC XY:
3
AN XY:
85578
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
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:
0.0000319
Gnomad OTH exome
AF:
0.000228
GnomAD4 exome
AF:
0.00000570
AC:
8
AN:
1403862
Hom.:
0
Cov.:
32
AF XY:
0.0000101
AC XY:
7
AN XY:
693126
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
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:
0.00000739
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsOct 21, 2024The c.1117G>A (p.A373T) alteration is located in exon 10 (coding exon 10) of the PHF21B gene. This alteration results from a G to A substitution at nucleotide position 1117, causing the alanine (A) at amino acid position 373 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Uncertain
0.012
T
BayesDel_noAF
Benign
-0.22
CADD
Uncertain
25
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.0097
.;.;T;.
Eigen
Uncertain
0.59
Eigen_PC
Uncertain
0.53
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Uncertain
0.97
D;D;D;D
M_CAP
Benign
0.018
T
MetaRNN
Uncertain
0.50
D;D;D;D
MetaSVM
Benign
-0.39
T
MutationAssessor
Uncertain
2.0
.;.;M;.
PrimateAI
Uncertain
0.52
T
PROVEAN
Benign
-1.4
N;.;N;.
REVEL
Benign
0.27
Sift
Benign
0.082
T;.;D;.
Sift4G
Benign
0.070
T;T;T;T
Polyphen
1.0
D;.;D;D
Vest4
0.63
MutPred
0.43
.;.;Gain of phosphorylation at T369 (P = 0.1133);.;
MVP
0.17
MPC
0.36
ClinPred
0.60
D
GERP RS
4.0
Varity_R
0.25
gMVP
0.33

Splicing

Name
Calibrated prediction
Score
Prediction
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

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

Other links and lift over

dbSNP: rs750532972; hg19: chr22-45283923; API