chr8-132826057-C-A

Variant names:

• chr8-132826057-C-A
• rs10505601
• NM_016018.5:c.1744+686C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_016018.5(PHF20L1):​c.1744+686C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,024 control chromosomes in the GnomAD database, including 1,027 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 0.10 (1027 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PHF20L1 NM_016018.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.666
• Publications: 5 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]

ENSG00000270137 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF20L1	NM_016018.5	c.1744+686C>A		intron_variant	Intron 14 of 20	ENST00000395386.7	NP_057102.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF20L1	ENST00000395386.7	c.1744+686C>A		intron_variant	Intron 14 of 20	5	NM_016018.5	ENSP00000378784.2

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15440 AN: 151906 Hom.: 1030 Cov.: 33

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.0935

Gnomad OTH AF: 0.113

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.102 AC: 15440 AN: 152024 Hom.: 1027 Cov.: 33 AF XY: 0.105 AC XY: 7832 AN XY: 74286

African (AFR) AF: 0.0573 AC: 2380 AN: 41514

American (AMR) AF: 0.149 AC: 2269 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3466

East Asian (EAS) AF: 0.355 AC: 1824 AN: 5132

South Asian (SAS) AF: 0.140 AC: 676 AN: 4824

European-Finnish (FIN) AF: 0.0951 AC: 1006 AN: 10574

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.0935 AC: 6354 AN: 67940

Other (OTH) AF: 0.112 AC: 237 AN: 2112

Alfa AF: 0.0955 Hom.: 353

Bravo AF: 0.104

Asia WGS AF: 0.197 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	2.8
DANN	Benign	0.89
PhyloP100		0.67
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: rs10505601; hg19: chr8-133838302;