NM_001080533.3:c.*2780A>G

Variant names:

• chr12-120722812-A-G
• rs2066938
• NM_001080533.3:c.*2780A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 60 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080533.3. 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
	UNC119B	NM_001080533.3	MANE Select	c.*2780A>G		3_prime_UTR	Exon 5 of 5	NP_001074002.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UNC119B	ENST00000344651.5	TSL:2 MANE Select	c.*2780A>G		3_prime_UTR	Exon 5 of 5	ENSP00000344942.4
	UNC119B	ENST00000718081.1		n.*3333A>G		non_coding_transcript_exon	Exon 5 of 5	ENSP00000520659.1
	UNC119B	ENST00000718083.1		n.*3162A>G		non_coding_transcript_exon	Exon 5 of 5	ENSP00000520661.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.222 AC: 9209 AN: 41516

American (AMR) AF: 0.289 AC: 4418 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1154 AN: 3470

East Asian (EAS) AF: 0.0667 AC: 346 AN: 5184

South Asian (SAS) AF: 0.257 AC: 1243 AN: 4832

European-Finnish (FIN) AF: 0.260 AC: 2757 AN: 10606

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17629 AN: 68000

Other (OTH) AF: 0.281 AC: 594 AN: 2114

Alfa AF: 0.258 Hom.: 23964

Bravo AF: 0.248

Asia WGS AF: 0.201 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		-0.24
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: rs2066938; hg19: chr12-121160615;