rs2274276

Variant names:

• chr13-49521817-C-A
• rs2274276
• NM_001040443.3:c.506-226C>A

Your query was ambiguous. Multiple possible variants found:

• chr13-49521817-C-A
• chr13-49521817-C-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.506-226C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000133 in 150,408 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: not found (cov: 32)
  • Exomes 𝑓: 0.000013 (0 hom.)
• Consequence: PHF11 NM_001040443.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11
• 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: 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=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF11	NM_001040443.3	c.506-226C>A		intron_variant	Intron 5 of 9	ENST00000378319.8	NP_001035533.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF11	ENST00000378319.8	c.506-226C>A		intron_variant	Intron 5 of 9	1	NM_001040443.3	ENSP00000367570.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.0000133 AC: 2 AN: 150408 Hom.: 0 AF XY: 0.0000252 AC XY: 2 AN XY: 79226

African (AFR) AF: 0.00 AC: 0 AN: 3992

American (AMR) AF: 0.00 AC: 0 AN: 3836

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5118

East Asian (EAS) AF: 0.00 AC: 0 AN: 9940

South Asian (SAS) AF: 0.00 AC: 0 AN: 12358

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 13316

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 698

European-Non Finnish (NFE) AF: 0.0000217 AC: 2 AN: 92056

Other (OTH) AF: 0.00 AC: 0 AN: 9094

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.3
DANN	Benign	0.63
PhyloP100		2.1

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: rs2274276; hg19: chr13-50095953;