chr11-125296916-G-A

Variant names:

• chr11-125296916-G-A
• rs4935917
• NM_001382323.2:c.-129-34903G>A

Variant summary

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

The NM_001382323.2(PKNOX2):​c.-129-34903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,154 control chromosomes in the GnomAD database, including 4,272 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 0.21 (4272 hom., cov: 33)
• Consequence: PKNOX2 NM_001382323.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 4 publications found

Genes affected

PKNOX2 (HGNC:16714): (PBX/knotted 1 homeobox 2) Homeodomain proteins are sequence-specific transcription factors that share a highly conserved DNA-binding domain and play fundamental roles in cell proliferation, differentiation, and death. PKNOX2 belongs to the TALE (3-amino acid loop extension) class of homeodomain proteins characterized by a 3-amino acid extension between alpha helices 1 and 2 within the homeodomain (Imoto et al., 2001 [PubMed 11549286]).[supplied by OMIM, Oct 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001382323.2. 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
	PKNOX2	NM_001382323.2	MANE Select	c.-129-34903G>A		intron	N/A	NP_001369252.1
	PKNOX2	NM_001382324.1		c.-202-34903G>A		intron	N/A	NP_001369253.1
	PKNOX2	NM_001382325.1		c.-22-54368G>A		intron	N/A	NP_001369254.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKNOX2	ENST00000298282.14	TSL:1 MANE Select	c.-129-34903G>A		intron	N/A	ENSP00000298282.8
	PKNOX2	ENST00000878499.1		c.-129-34903G>A		intron	N/A	ENSP00000548558.1
	PKNOX2	ENST00000878493.1		c.-129-34903G>A		intron	N/A	ENSP00000548552.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31912 AN: 152036 Hom.: 4263 Cov.: 33

Gnomad AFR AF: 0.0525

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.210 AC: 31932 AN: 152154 Hom.: 4272 Cov.: 33 AF XY: 0.209 AC XY: 15519 AN XY: 74356

African (AFR) AF: 0.0524 AC: 2178 AN: 41532

American (AMR) AF: 0.241 AC: 3686 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1015 AN: 3472

East Asian (EAS) AF: 0.136 AC: 704 AN: 5176

South Asian (SAS) AF: 0.327 AC: 1571 AN: 4810

European-Finnish (FIN) AF: 0.240 AC: 2537 AN: 10578

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.284 AC: 19336 AN: 67998

Other (OTH) AF: 0.260 AC: 551 AN: 2116

Alfa AF: 0.266 Hom.: 6462

Bravo AF: 0.203

Asia WGS AF: 0.242 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.45
DANN	Benign	0.55
PhyloP100		-0.45
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: rs4935917; hg19: chr11-125166812;