chr16-1413429-A-G

Variant names:

• chr16-1413429-A-G
• rs11248877
• NM_001372107.1:c.287+417T>C

Variant summary

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

The NM_001372107.1(UNKL):​c.287+417T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.943 in 152,110 control chromosomes in the GnomAD database, including 67,706 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 0.94 (67706 hom., cov: 30)
• Consequence: UNKL NM_001372107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 4 publications found

Genes affected

UNKL (HGNC:14184): (unk like zinc finger) This gene encodes a RING finger protein that may function in Rac signaling. It can bind to Brg/Brm-associated factor 60b and can promote its ubiquitination. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jun 2013]

UNKL Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001372107.1. 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
	UNKL	NM_001372107.1	MANE Select	c.287+417T>C		intron	N/A	NP_001359036.1
	UNKL	NM_001193388.4		c.287+417T>C		intron	N/A	NP_001180317.2
	UNKL	NM_001037125.4		c.287+417T>C		intron	N/A	NP_001032202.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UNKL	ENST00000389221.9	TSL:5 MANE Select	c.287+417T>C		intron	N/A	ENSP00000373873.6
	UNKL	ENST00000301712.5	TSL:1	c.287+417T>C		intron	N/A	ENSP00000301712.5
	UNKL	ENST00000876325.1		c.287+417T>C		intron	N/A	ENSP00000546384.1

Frequencies

GnomAD3 genomes AF: 0.943 AC: 143330 AN: 151992 Hom.: 67645 Cov.: 30

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.943 AC: 143450 AN: 152110 Hom.: 67706 Cov.: 30 AF XY: 0.945 AC XY: 70283 AN XY: 74370

African (AFR) AF: 0.970 AC: 40250 AN: 41478

American (AMR) AF: 0.950 AC: 14510 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3200 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5167 AN: 5170

South Asian (SAS) AF: 0.960 AC: 4627 AN: 4820

European-Finnish (FIN) AF: 0.945 AC: 10004 AN: 10584

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.919 AC: 62514 AN: 68002

Other (OTH) AF: 0.959 AC: 2025 AN: 2112

Alfa AF: 0.931 Hom.: 8190

Bravo AF: 0.946

Asia WGS AF: 0.985 AC: 3425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.27
DANN	Benign	0.17
PhyloP100		-1.3
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: rs11248877; hg19: chr16-1463430;