rs7329078

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr13-49518350-T-A
• chr13-49518350-T-C
• chr13-49518350-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001040443.3(PHF11):​c.458+199T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PHF11 NM_001040443.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 6 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040443.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF11	NM_001040443.3	MANE Select	c.458+199T>A		intron	N/A	NP_001035533.1
	SETDB2-PHF11	NM_001320727.2		c.1940+199T>A		intron	N/A	NP_001307656.1
	PHF11	NM_001040444.3		c.341+199T>A		intron	N/A	NP_001035534.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF11	ENST00000378319.8	TSL:1 MANE Select	c.458+199T>A		intron	N/A	ENSP00000367570.3
	PHF11	ENST00000488958.5	TSL:1	c.341+199T>A		intron	N/A	ENSP00000417539.1
	PHF11	ENST00000465045.5	TSL:1	n.341+199T>A		intron	N/A	ENSP00000418630.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 123150 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 64670

African (AFR) AF: 0.00 AC: 0 AN: 3810

American (AMR) AF: 0.00 AC: 0 AN: 4330

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4556

East Asian (EAS) AF: 0.00 AC: 0 AN: 12148

South Asian (SAS) AF: 0.00 AC: 0 AN: 1294

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6082

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 596

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 82278

Other (OTH) AF: 0.00 AC: 0 AN: 8056

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 16700

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.29
PhyloP100		0.18

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: rs7329078; hg19: chr13-50092486;