rs10505600

Variant names:

• chr8-132800617-C-G
• rs10505600
• NM_016018.5:c.507+1445C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016018.5(PHF20L1):​c.507+1445C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 151,576 control chromosomes in the GnomAD database, including 1,480 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 0.13 (1480 hom., cov: 31)
• Consequence: PHF20L1 NM_016018.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946

Genes affected

PHF20L1 (HGNC:24280): (PHD finger protein 20 like 1) Predicted to enable metal ion binding activity. Predicted to be involved in histone acetylation and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of NSL complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF20L1	NM_016018.5	c.507+1445C>G		intron_variant	Intron 6 of 20	ENST00000395386.7	NP_057102.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF20L1	ENST00000395386.7	c.507+1445C>G		intron_variant	Intron 6 of 20	5	NM_016018.5	ENSP00000378784.2

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19579 AN: 151458 Hom.: 1482 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.129 AC: 19594 AN: 151576 Hom.: 1480 Cov.: 31 AF XY: 0.132 AC XY: 9747 AN XY: 74064

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0951

Gnomad4 NFE AF: 0.0935

Gnomad4 OTH AF: 0.137

Alfa AF: 0.104 Hom.: 115

Bravo AF: 0.136

Asia WGS AF: 0.210 AC: 730 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.57

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

Other links and lift over

dbSNP: rs10505600; hg19: chr8-133812863;