13-49526937-C-T

Variant names:

• chr13-49526937-C-T
• rs2980
• NM_001040443.3:c.841+479C>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+479C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,610 control chromosomes in the GnomAD database, including 18,139 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 (18139 hom., cov: 30)
• Consequence: PHF11 NM_001040443.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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 (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF11	NM_001040443.3	c.841+479C>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.841+479C>T		intron_variant	Intron 9 of 9	1	NM_001040443.3	ENSP00000367570.3

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73184 AN: 151492 Hom.: 18129 Cov.: 30

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.483 AC: 73226 AN: 151610 Hom.: 18139 Cov.: 30 AF XY: 0.480 AC XY: 35509 AN XY: 74046

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.508

Alfa AF: 0.518 Hom.: 9437

Bravo AF: 0.483

Asia WGS AF: 0.390 AC: 1354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.48

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: rs2980; hg19: chr13-50101073;