rs2472537

Positions:

• chr8-132848400-G-A
• chr8-132848400-G-C
• chr8-132848400-G-T

Variant summary

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

The NM_016018.5(PHF20L1):​c.*2477G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,508 control chromosomes in the GnomAD database, including 53,002 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 0.83 (52859 hom., cov: 32)
  • Exomes 𝑓: 0.81 (143 hom.)
• Consequence: PHF20L1 NM_016018.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

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]

PHF20L1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF20L1	NM_016018.5	c.*2477G>A		3_prime_UTR_variant	21/21	ENST00000395386.7	NP_057102.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHF20L1	ENST00000395386.7	c.*2477G>A		3_prime_UTR_variant	21/21	5	NM_016018.5	ENSP00000378784.2
PHF20L1	ENST00000395390.6	c.*2477G>A		3_prime_UTR_variant	19/19	5		ENSP00000378788.2

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126268 AN: 151958 Hom.: 52801 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.829

GnomAD4 exome AF: 0.810 AC: 350 AN: 432 Hom.: 143 Cov.: 0 AF XY: 0.823 AC XY: 214 AN XY: 260

Gnomad4 FIN exome AF: 0.808

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.831 AC: 126383 AN: 152076 Hom.: 52859 Cov.: 32 AF XY: 0.834 AC XY: 62017 AN XY: 74348

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.830

Alfa AF: 0.797 Hom.: 31224

Bravo AF: 0.832

Asia WGS AF: 0.895 AC: 3105 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2472537; hg19: chr8-133860645;