13-49515708-C-T

Variant names:

• chr13-49515708-C-T
• rs9568232
• NM_001040443.3:c.325-2310C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PHF11	NM_001040443.3	c.325-2310C>T		intron_variant	Intron 3 of 9	ENST00000378319.8	NP_001035533.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF11	ENST00000378319.8	c.325-2310C>T		intron_variant	Intron 3 of 9	1	NM_001040443.3	ENSP00000367570.3

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

African (AFR) AF: 0.391 AC: 16162 AN: 41326

American (AMR) AF: 0.152 AC: 2319 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0289 AC: 100 AN: 3466

East Asian (EAS) AF: 0.216 AC: 1114 AN: 5162

South Asian (SAS) AF: 0.218 AC: 1046 AN: 4800

European-Finnish (FIN) AF: 0.0925 AC: 978 AN: 10572

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0664 AC: 4515 AN: 68006

Other (OTH) AF: 0.138 AC: 290 AN: 2104

Alfa AF: 0.0954 Hom.: 2148

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
PhyloP100		0.80
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: rs9568232; hg19: chr13-50089844;