13-49496108-GGGGCGGGCGGGCGGGC-GGGGCGGGCGGGC

Variant names:

• chr13-49496108-GGGGC-G
• rs370049093
• NM_001040443.3:c.94+33_94+36delCGGG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001419873.1(PHF11):​c.-506_-503delCGGG variant causes a 5 prime UTR 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_001419873.1 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0640
• Publications: 1 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 -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001419873.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF11	NM_001040443.3	MANE Select	c.94+33_94+36delCGGG		intron	N/A	NP_001035533.1	Q9UIL8-1
	PHF11	NM_001419873.1		c.-506_-503delCGGG		5_prime_UTR	Exon 1 of 11	NP_001406802.1	Q9UIL8-2
	PHF11	NM_001419874.1		c.-540_-537delCGGG		5_prime_UTR	Exon 1 of 11	NP_001406803.1	Q9UIL8-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF11	ENST00000378319.8	TSL:1 MANE Select	c.94+14_94+17delGGGC		intron	N/A	ENSP00000367570.3	Q9UIL8-1
	PHF11	ENST00000941732.1		c.94+14_94+17delGGGC		intron	N/A	ENSP00000611791.1
	PHF11	ENST00000873990.1		c.94+14_94+17delGGGC		intron	N/A	ENSP00000544049.1

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

GnomAD2 exomes AF: 0.0426 AC: 4 AN: 94 AF XY: 0.0645

Gnomad AMR exome AF: 0.00

Gnomad ASJ 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

African (AFR) AF: 0.473 AC: 5518 AN: 11672

American (AMR) AF: 0.719 AC: 5024 AN: 6986

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 6726 AN: 10424

East Asian (EAS) AF: 0.844 AC: 18374 AN: 21766

South Asian (SAS) AF: 0.461 AC: 10299 AN: 22344

European-Finnish (FIN) AF: 0.770 AC: 18115 AN: 23522

Middle Eastern (MID) AF: 0.584 AC: 1035 AN: 1772

European-Non Finnish (NFE) AF: 0.442 AC: 184431 AN: 417388

Other (OTH) AF: 0.553 AC: 13999 AN: 25322

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

African (AFR) AF: 0.672 AC: 27532 AN: 40950

American (AMR) AF: 0.744 AC: 11287 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2478 AN: 3464

East Asian (EAS) AF: 0.812 AC: 3980 AN: 4904

South Asian (SAS) AF: 0.607 AC: 2892 AN: 4764

European-Finnish (FIN) AF: 0.783 AC: 7946 AN: 10150

Middle Eastern (MID) AF: 0.707 AC: 205 AN: 290

European-Non Finnish (NFE) AF: 0.713 AC: 47985 AN: 67296

Other (OTH) AF: 0.722 AC: 1510 AN: 2092

Alfa AF: 0.607 Hom.: 1272

Asia WGS AF: 0.673 AC: 2279 AN: 3390

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.064
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: rs370049093; hg19: chr13-50070244; COSMIC: COSV107357800; COSMIC: COSV107357800;