13-49524240-G-T

Position:

• chr13-49524240-G-T

Variant summary

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

The NM_001040443.3(PHF11):​c.769+24G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,556,822 control chromosomes in the GnomAD database, including 12,091 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 0.16 (2884 hom., cov: 31)
  • Exomes 𝑓: 0.095 (9207 hom.)
• Consequence: PHF11 NM_001040443.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF11	NM_001040443.3	c.769+24G>T		intron_variant		ENST00000378319.8	NP_001035533.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHF11	ENST00000378319.8	c.769+24G>T		intron_variant		1	NM_001040443.3	ENSP00000367570.3

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23608 AN: 150206 Hom.: 2874 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.0474

Gnomad AMR AF: 0.0962

Gnomad ASJ AF: 0.0612

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.0749

Gnomad MID AF: 0.0710

Gnomad NFE AF: 0.0726

Gnomad OTH AF: 0.112

GnomAD3 exomes AF: 0.130 AC: 29685 AN: 227738 Hom.: 2776 AF XY: 0.131 AC XY: 16264 AN XY: 124368

Gnomad AFR exome AF: 0.342

Gnomad AMR exome AF: 0.118

Gnomad ASJ exome AF: 0.0645

Gnomad EAS exome AF: 0.216

Gnomad SAS exome AF: 0.254

Gnomad FIN exome AF: 0.0804

Gnomad NFE exome AF: 0.0781

Gnomad OTH exome AF: 0.0990

GnomAD4 exome AF: 0.0949 AC: 133426 AN: 1406500 Hom.: 9207 Cov.: 24 AF XY: 0.0989 AC XY: 69397 AN XY: 701402

Gnomad4 AFR exome AF: 0.335

Gnomad4 AMR exome AF: 0.107

Gnomad4 ASJ exome AF: 0.0649

Gnomad4 EAS exome AF: 0.233

Gnomad4 SAS exome AF: 0.246

Gnomad4 FIN exome AF: 0.0810

Gnomad4 NFE exome AF: 0.0720

Gnomad4 OTH exome AF: 0.106

GnomAD4 genome AF: 0.157 AC: 23669 AN: 150322 Hom.: 2884 Cov.: 31 AF XY: 0.159 AC XY: 11662 AN XY: 73214

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.0959

Gnomad4 ASJ AF: 0.0612

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.0749

Gnomad4 NFE AF: 0.0726

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0828 Hom.: 1040

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.22

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: rs7332573; hg19: chr13-50098376;