13-49496108-GGGGC-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001040443.3(PHF11):c.94+33_94+36del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 691,168 control chromosomes in the GnomAD database, including 136,139 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.71 (37995 hom., cov: 0)
  • Exomes 𝑓: 0.49 (98144 hom.)
• Consequence: PHF11 NM_001040443.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0640

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 -10 ACMG points.

• BP6: Variant 13-49496108-GGGGC-G is Benign according to our data. Variant chr13-49496108-GGGGC-G is described in ClinVar as [Benign]. Clinvar id is 2975967.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF11	NM_001040443.3	c.94+33_94+36del		intron_variant		ENST00000378319.8
SETDB2-PHF11	NR_135324.2	n.2662+5218_2662+5221del		intron_variant, non_coding_transcript_variant
SETDB2-PHF11	NM_001320727.2	c.1576+10405_1576+10408del		intron_variant
PHF11	NR_135322.2	n.143+33_143+36del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF11	ENST00000378319.8	c.94+33_94+36del		intron_variant		1	NM_001040443.3	P2

Frequencies

GnomAD3 genomes AF: 0.710 AC: 106375 AN: 149862 Hom.: 37957 Cov.: 0

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.708

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.725

GnomAD3 exomes AF: 0.0426 AC: 4 AN: 94 Hom.: 2 AF XY: 0.0645 AC XY: 4 AN XY: 62

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.105

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.487 AC: 263521 AN: 541196 Hom.: 98144 AF XY: 0.501 AC XY: 134315 AN XY: 267862

Gnomad4 AFR exome AF: 0.473

Gnomad4 AMR exome AF: 0.719

Gnomad4 ASJ exome AF: 0.645

Gnomad4 EAS exome AF: 0.844

Gnomad4 SAS exome AF: 0.461

Gnomad4 FIN exome AF: 0.770

Gnomad4 NFE exome AF: 0.442

Gnomad4 OTH exome AF: 0.553

GnomAD4 genome AF: 0.710 AC: 106455 AN: 149972 Hom.: 37995 Cov.: 0 AF XY: 0.712 AC XY: 52123 AN XY: 73158

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.722

Asia WGS AF: 0.673 AC: 2279 AN: 3390

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 17, 2024

- -

Computational scores

Source: dbNSFP v4.3

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: rs370049093; hg19: chr13-50070244;