13-49515708-C-T

Variant summary

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

The NM_001040443.3(PHF11):c.325-2310C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,900 control chromosomes in the GnomAD database, including 3,811 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 0.17 (3811 hom., cov: 30)
• Consequence: PHF11 NM_001040443.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.801

Genes affected

PHF11 (HGNC:17024): (PHD finger protein 11) This gene encodes a protein containing a PHD (plant homeodomain) type zinc finger. This gene has been identified in some studies as a candidate gene for asthma. Naturally-occurring readthrough transcription may occur from the upstream SETDB2 (SET domain bifurcated 2) gene to this locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

SETDB2-PHF11 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF11	NM_001040443.3	c.325-2310C>T		intron_variant		ENST00000378319.8
SETDB2-PHF11	NR_135324.2	n.2771-2310C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF11	ENST00000378319.8	c.325-2310C>T		intron_variant		1	NM_001040443.3	P2

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26531 AN: 151782 Hom.: 3801 Cov.: 30

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0289

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0664

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.175 AC: 26575 AN: 151900 Hom.: 3811 Cov.: 30 AF XY: 0.177 AC XY: 13141 AN XY: 74236

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0289

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.0925

Gnomad4 NFE AF: 0.0664

Gnomad4 OTH AF: 0.138

Alfa AF: 0.0860 Hom.: 1345

Bravo AF: 0.185

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.4
Dann	Benign	0.77

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: rs9568232; hg19: chr13-50089844;