chr22-44999021-C-G

Variant names:

• chr22-44999021-C-G
• rs5765113
• NM_138415.5:c.120+9524G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138415.5(PHF21B):​c.120+9524G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 152,232 control chromosomes in the GnomAD database, including 64,826 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.92 (64826 hom., cov: 31)
• Consequence: PHF21B NM_138415.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138415.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF21B	NM_138415.5	MANE Select	c.120+9524G>C		intron	N/A	NP_612424.1	A0A0S2Z6R3
	PHF21B	NM_001135862.3		c.120+9524G>C		intron	N/A	NP_001129334.1	A0A0S2Z665
	PHF21B	NM_001413063.1		c.120+9524G>C		intron	N/A	NP_001399992.1	Q96EK2-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF21B	ENST00000313237.10	TSL:1 MANE Select	c.120+9524G>C		intron	N/A	ENSP00000324403.5	Q96EK2-1
	PHF21B	ENST00000629843.3	TSL:1	c.120+9524G>C		intron	N/A	ENSP00000487086.1	Q96EK2-3
	PHF21B	ENST00000420689.2	TSL:5	c.84+9524G>C		intron	N/A	ENSP00000401294.2	Q96EK2-4

Frequencies

GnomAD3 genomes AF: 0.920 AC: 140005 AN: 152114 Hom.: 64797 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.928

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.920 AC: 140088 AN: 152232 Hom.: 64826 Cov.: 31 AF XY: 0.922 AC XY: 68622 AN XY: 74430

African (AFR) AF: 0.814 AC: 33807 AN: 41522

American (AMR) AF: 0.949 AC: 14507 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3108 AN: 3472

East Asian (EAS) AF: 0.951 AC: 4905 AN: 5160

South Asian (SAS) AF: 0.975 AC: 4706 AN: 4826

European-Finnish (FIN) AF: 0.966 AC: 10249 AN: 10606

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65694 AN: 68036

Other (OTH) AF: 0.926 AC: 1956 AN: 2112

Alfa AF: 0.939 Hom.: 7946

Bravo AF: 0.915

Asia WGS AF: 0.912 AC: 3172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.022
DANN	Benign	0.46
PhyloP100		-0.52
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5765113; hg19: chr22-45394902;