rs10485511

Variant names:

• chr20-35859520-C-G
• rs10485511
• NM_016436.5:c.420+1139C>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.420+1139C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0439 in 151,074 control chromosomes in the GnomAD database, including 183 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 0.044 (183 hom., cov: 31)
• Consequence: PHF20 NM_016436.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 0 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.081 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF20	NM_016436.5	c.420+1139C>G		intron_variant	Intron 5 of 17	ENST00000374012.8	NP_057520.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF20	ENST00000374012.8	c.420+1139C>G		intron_variant	Intron 5 of 17	1	NM_016436.5	ENSP00000363124.3

Frequencies

GnomAD3 genomes AF: 0.0439 AC: 6635 AN: 150996 Hom.: 183 Cov.: 31

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0281

Gnomad ASJ AF: 0.0529

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0119

Gnomad FIN AF: 0.0464

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.0443

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

GnomAD4 genome AF: 0.0439 AC: 6634 AN: 151074 Hom.: 183 Cov.: 31 AF XY: 0.0432 AC XY: 3187 AN XY: 73740

African (AFR) AF: 0.0833 AC: 3430 AN: 41154

American (AMR) AF: 0.0279 AC: 423 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.0529 AC: 183 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5146

South Asian (SAS) AF: 0.0115 AC: 55 AN: 4780

European-Finnish (FIN) AF: 0.0464 AC: 474 AN: 10216

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0284 AC: 1930 AN: 67852

Other (OTH) AF: 0.0439 AC: 92 AN: 2094

Alfa AF: 0.0394 Hom.: 16

Bravo AF: 0.0437

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.61
PhyloP100		0.074
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: rs10485511; hg19: chr20-34447442;