rs11906854

Variant names:

• chr20-35795712-A-G
• rs11906854
• NM_016436.5:c.-32-5779A>G

Variant summary

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

The NM_016436.5(PHF20):​c.-32-5779A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,054 control chromosomes in the GnomAD database, including 2,250 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 0.17 (2250 hom., cov: 31)
• Consequence: PHF20 NM_016436.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828
• Publications: 27 publications found

Genes affected

PHF20 (HGNC:16098): (PHD finger protein 20) Predicted to enable DNA binding activity and metal ion binding activity. Involved in histone H4-K16 acetylation; histone H4-K5 acetylation; and histone H4-K8 acetylation. Located in cytosol; nuclear membrane; and nucleoplasm. Part of MLL1 complex and histone acetyltransferase complex. [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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF20	NM_016436.5	c.-32-5779A>G		intron_variant	Intron 1 of 17	ENST00000374012.8	NP_057520.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF20	ENST00000374012.8	c.-32-5779A>G		intron_variant	Intron 1 of 17	1	NM_016436.5	ENSP00000363124.3

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25638 AN: 151936 Hom.: 2249 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.169 AC: 25648 AN: 152054 Hom.: 2250 Cov.: 31 AF XY: 0.168 AC XY: 12521 AN XY: 74314

African (AFR) AF: 0.235 AC: 9732 AN: 41472

American (AMR) AF: 0.154 AC: 2348 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 584 AN: 3468

East Asian (EAS) AF: 0.121 AC: 625 AN: 5186

South Asian (SAS) AF: 0.175 AC: 844 AN: 4812

European-Finnish (FIN) AF: 0.147 AC: 1559 AN: 10574

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9434 AN: 67988

Other (OTH) AF: 0.171 AC: 362 AN: 2112

Alfa AF: 0.150 Hom.: 4170

Bravo AF: 0.169

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.43
PhyloP100		-0.83
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: rs11906854; hg19: chr20-34383634;