NM_001040443.3:c.842-428C>T

Variant names:

• chr13-49528083-C-T
• rs9526569
• NM_001040443.3:c.842-428C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040443.3(PHF11):​c.842-428C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,960 control chromosomes in the GnomAD database, including 28,565 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 0.61 (28565 hom., cov: 32)
• Consequence: PHF11 NM_001040443.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407
• Publications: 10 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF11	NM_001040443.3	c.842-428C>T		intron_variant	Intron 9 of 9	ENST00000378319.8	NP_001035533.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF11	ENST00000378319.8	c.842-428C>T		intron_variant	Intron 9 of 9	1	NM_001040443.3	ENSP00000367570.3

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92695 AN: 151842 Hom.: 28539 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.610 AC: 92761 AN: 151960 Hom.: 28565 Cov.: 32 AF XY: 0.612 AC XY: 45460 AN XY: 74258

African (AFR) AF: 0.560 AC: 23167 AN: 41400

American (AMR) AF: 0.675 AC: 10313 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2102 AN: 3464

East Asian (EAS) AF: 0.801 AC: 4150 AN: 5184

South Asian (SAS) AF: 0.542 AC: 2609 AN: 4812

European-Finnish (FIN) AF: 0.638 AC: 6725 AN: 10540

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41777 AN: 67968

Other (OTH) AF: 0.621 AC: 1310 AN: 2108

Alfa AF: 0.614 Hom.: 77054

Bravo AF: 0.613

Asia WGS AF: 0.649 AC: 2253 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

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: rs9526569; hg19: chr13-50102219;