rs2981

Positions:

• chr13-49526958-G-A
• chr13-49526958-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.841+500G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,312 control chromosomes in the GnomAD database, including 18,033 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 0.48 (18033 hom., cov: 29)
• Consequence: PHF11 NM_001040443.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.619

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF11	NM_001040443.3	c.841+500G>A		intron_variant		ENST00000378319.8	NP_001035533.1
SETDB2-PHF11	NR_135324.2	n.3452+500G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHF11	ENST00000378319.8	c.841+500G>A		intron_variant		1	NM_001040443.3	ENSP00000367570	P2

Frequencies

GnomAD3 genomes AF: 0.482 AC: 72806 AN: 151194 Hom.: 18023 Cov.: 29

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.508

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.481 AC: 72848 AN: 151312 Hom.: 18033 Cov.: 29 AF XY: 0.478 AC XY: 35330 AN XY: 73862

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.505

Alfa AF: 0.534 Hom.: 46136

Bravo AF: 0.481

Asia WGS AF: 0.391 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.71

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: rs2981; hg19: chr13-50101094;