13-49518350-T-C

Variant names:

• chr13-49518350-T-C
• rs7329078
• NM_001040443.3:c.458+199T>C

Variant summary

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

The NM_001040443.3(PHF11):​c.458+199T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 274,210 control chromosomes in the GnomAD database, including 58,378 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 0.60 (27697 hom., cov: 30)
  • Exomes 𝑓: 0.70 (30681 hom.)
• Consequence: PHF11 NM_001040443.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

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 (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF11	NM_001040443.3	c.458+199T>C		intron_variant	Intron 4 of 9	ENST00000378319.8	NP_001035533.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF11	ENST00000378319.8	c.458+199T>C		intron_variant	Intron 4 of 9	1	NM_001040443.3	ENSP00000367570.3

Frequencies

GnomAD3 genomes AF: 0.601 AC: 90838 AN: 151114 Hom.: 27658 Cov.: 30

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.619

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.600

GnomAD4 exome AF: 0.705 AC: 86646 AN: 122978 Hom.: 30681 Cov.: 2 AF XY: 0.702 AC XY: 45338 AN XY: 64586

Gnomad4 AFR exome AF: 0.605

Gnomad4 AMR exome AF: 0.728

Gnomad4 ASJ exome AF: 0.662

Gnomad4 EAS exome AF: 0.898

Gnomad4 SAS exome AF: 0.615

Gnomad4 FIN exome AF: 0.728

Gnomad4 NFE exome AF: 0.683

Gnomad4 OTH exome AF: 0.690

GnomAD4 genome AF: 0.601 AC: 90920 AN: 151232 Hom.: 27697 Cov.: 30 AF XY: 0.603 AC XY: 44565 AN XY: 73862

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.598

Alfa AF: 0.604 Hom.: 15167

Bravo AF: 0.605

Asia WGS AF: 0.651 AC: 2246 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.46

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: rs7329078; hg19: chr13-50092486;