rs2472537

Variant names:

• chr8-132848400-G-A
• rs2472537
• NM_016018.5:c.*2477G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016018.5. 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
	PHF20L1	NM_016018.5	MANE Select	c.*2477G>A		3_prime_UTR	Exon 21 of 21	NP_057102.4
	PHF20L1	NM_001438309.1		c.*2477G>A		3_prime_UTR	Exon 21 of 21	NP_001425238.1
	PHF20L1	NM_001438310.1		c.*2477G>A		3_prime_UTR	Exon 21 of 21	NP_001425239.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF20L1	ENST00000395386.7	TSL:5 MANE Select	c.*2477G>A		3_prime_UTR	Exon 21 of 21	ENSP00000378784.2
	PHF20L1	ENST00000972150.1		c.*2477G>A		3_prime_UTR	Exon 21 of 21	ENSP00000642209.1
	PHF20L1	ENST00000395390.6	TSL:5	c.*2477G>A		3_prime_UTR	Exon 19 of 19	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.808 AC: 344 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 1.00 AC: 4 AN: 4

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

African (AFR) AF: 0.930 AC: 38633 AN: 41548

American (AMR) AF: 0.771 AC: 11767 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2795 AN: 3472

East Asian (EAS) AF: 0.950 AC: 4927 AN: 5184

South Asian (SAS) AF: 0.854 AC: 4114 AN: 4818

European-Finnish (FIN) AF: 0.814 AC: 8610 AN: 10578

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.779 AC: 52906 AN: 67904

Other (OTH) AF: 0.830 AC: 1752 AN: 2110

Alfa AF: 0.798 Hom.: 42311

Bravo AF: 0.832

Asia WGS AF: 0.895 AC: 3105 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		0.028
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2472537; hg19: chr8-133860645;