rs7332573

chr13-49524240-G-Achr13-49524240-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001040443.3(PHF11):c.769+24G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000764 in 1,558,914 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00071 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00077 (0 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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF11	NM_001040443.3	c.769+24G>A		intron_variant		ENST00000378319.8
SETDB2-PHF11	NR_135324.2	n.3215+24G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF11	ENST00000378319.8	c.769+24G>A		intron_variant		1	NM_001040443.3	P2

Frequencies

GnomAD3 genomes AF: 0.000712 AC: 107 AN: 150284 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000978

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000998

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00468

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000886

Gnomad OTH AF: 0.00194

GnomAD3 exomes AF: 0.000746 AC: 170 AN: 227738 Hom.: 0 AF XY: 0.000724 AC XY: 90 AN XY: 124368

Gnomad AFR exome AF: 0.000207

Gnomad AMR exome AF: 0.000249

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00484

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000472

Gnomad NFE exome AF: 0.000735

Gnomad OTH exome AF: 0.000365

GnomAD4 exome AF: 0.000770 AC: 1084 AN: 1408516 Hom.: 0 Cov.: 24 AF XY: 0.000745 AC XY: 523 AN XY: 702310

Gnomad4 AFR exome AF: 0.0000642

Gnomad4 AMR exome AF: 0.000429

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00159

Gnomad4 SAS exome AF: 0.0000123

Gnomad4 FIN exome AF: 0.0000382

Gnomad4 NFE exome AF: 0.000873

Gnomad4 OTH exome AF: 0.00105

GnomAD4 genome AF: 0.000711 AC: 107 AN: 150398 Hom.: 0 Cov.: 31 AF XY: 0.000723 AC XY: 53 AN XY: 73264

Gnomad4 AFR AF: 0.0000975

Gnomad4 AMR AF: 0.000997

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00469

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000886

Gnomad4 OTH AF: 0.00192

Alfa AF: 0.0000194 Hom.: 1040

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.6
Dann	Benign	0.88

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;