rs2981

Variant names:

• chr13-49526958-G-A
• rs2981
• NM_001040443.3:c.841+500G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-49526958-G-A
• chr13-49526958-G-C
• chr13-49526958-G-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.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
• Publications: 27 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040443.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF11	NM_001040443.3	MANE Select	c.841+500G>A		intron	N/A	NP_001035533.1
	SETDB2-PHF11	NM_001320727.2		c.2323+500G>A		intron	N/A	NP_001307656.1
	PHF11	NM_001040444.3		c.724+500G>A		intron	N/A	NP_001035534.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF11	ENST00000378319.8	TSL:1 MANE Select	c.841+500G>A		intron	N/A	ENSP00000367570.3
	PHF11	ENST00000488958.5	TSL:1	c.724+500G>A		intron	N/A	ENSP00000417539.1
	PHF11	ENST00000465045.5	TSL:1	n.*208+500G>A		intron	N/A	ENSP00000418630.1

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

African (AFR) AF: 0.362 AC: 14939 AN: 41214

American (AMR) AF: 0.525 AC: 7981 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1882 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2406 AN: 5122

South Asian (SAS) AF: 0.319 AC: 1529 AN: 4792

European-Finnish (FIN) AF: 0.536 AC: 5570 AN: 10398

Middle Eastern (MID) AF: 0.593 AC: 172 AN: 290

European-Non Finnish (NFE) AF: 0.544 AC: 36913 AN: 67830

Other (OTH) AF: 0.505 AC: 1065 AN: 2108

Alfa AF: 0.523 Hom.: 74727

Bravo AF: 0.481

Asia WGS AF: 0.391 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.71
PhyloP100		0.62
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: rs2981; hg19: chr13-50101094;