rs11248877

chr16-1413429-A-Gchr16-1413429-A-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UNKL	NM_001372107.1	c.287+417T>C		intron_variant		ENST00000389221.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UNKL	ENST00000389221.9	c.287+417T>C		intron_variant		5	NM_001372107.1	P1

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

Gnomad4 AFR AF: 0.970

Gnomad4 AMR AF: 0.950

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.960

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.919

Gnomad4 OTH AF: 0.959

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.27
Dann	Benign	0.17

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: rs11248877; hg19: chr16-1463430;