chr12-120722812-A-G

Position:

• chr12-120722812-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080533.3(UNC119B):​c.*2780A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,230 control chromosomes in the GnomAD database, including 4,964 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 0.25 (4964 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: UNC119B NM_001080533.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

Genes affected

UNC119B (HGNC:16488): (unc-119 lipid binding chaperone B) Enables lipid binding activity. Involved in cilium assembly and lipoprotein transport. Located in ciliary transition zone. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000256569 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UNC119B	NM_001080533.3	c.*2780A>G		3_prime_UTR_variant	5/5	ENST00000344651.5	NP_001074002.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UNC119B	ENST00000344651.5	c.*2780A>G		3_prime_UTR_variant	5/5	2	NM_001080533.3	ENSP00000344942.4
ENSG00000256569	ENST00000544939.1	n.61+767T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37692 AN: 152108 Hom.: 4955 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.274

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.248 AC: 37715 AN: 152226 Hom.: 4964 Cov.: 33 AF XY: 0.251 AC XY: 18676 AN XY: 74422

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.0667

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.281

Alfa AF: 0.262 Hom.: 11765

Bravo AF: 0.248

Asia WGS AF: 0.201 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.54

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: rs2066938; hg19: chr12-121160615;