12-120713290-C-T

Variant names:

• chr12-120713290-C-T
• rs11829037
• NM_001080533.3:c.261C>T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001080533.3(UNC119B):​c.261C>T​(p.Pro87Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 1,610,150 control chromosomes in the GnomAD database, including 4,300 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 0.10 (2011 hom., cov: 33)
  • Exomes 𝑓: 0.022 (2289 hom.)
• Consequence: UNC119B NM_001080533.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14

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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP7: Synonymous conserved (PhyloP=-3.14 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UNC119B	NM_001080533.3	c.261C>T	p.Pro87Pro	synonymous_variant	Exon 2 of 5	ENST00000344651.5	NP_001074002.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UNC119B	ENST00000344651.5	c.261C>T	p.Pro87Pro	synonymous_variant	Exon 2 of 5	2	NM_001080533.3	ENSP00000344942.4
UNC119B	ENST00000539658.1	n.375C>T		non_coding_transcript_exon_variant	Exon 3 of 4	5		ENSP00000520658.1

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15335 AN: 151978 Hom.: 2007 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00860

Gnomad OTH AF: 0.0662

GnomAD3 exomes AF: 0.0502 AC: 12573 AN: 250558 Hom.: 1078 AF XY: 0.0423 AC XY: 5738 AN XY: 135512

Gnomad AFR exome AF: 0.308

Gnomad AMR exome AF: 0.0687

Gnomad ASJ exome AF: 0.0162

Gnomad EAS exome AF: 0.148

Gnomad SAS exome AF: 0.0216

Gnomad FIN exome AF: 0.0213

Gnomad NFE exome AF: 0.00879

Gnomad OTH exome AF: 0.0372

GnomAD4 exome AF: 0.0222 AC: 32355 AN: 1458054 Hom.: 2289 Cov.: 30 AF XY: 0.0210 AC XY: 15253 AN XY: 725252

Gnomad4 AFR exome AF: 0.311

Gnomad4 AMR exome AF: 0.0683

Gnomad4 ASJ exome AF: 0.0157

Gnomad4 EAS exome AF: 0.131

Gnomad4 SAS exome AF: 0.0231

Gnomad4 FIN exome AF: 0.0194

Gnomad4 NFE exome AF: 0.00701

Gnomad4 OTH exome AF: 0.0381

GnomAD4 genome AF: 0.101 AC: 15363 AN: 152096 Hom.: 2011 Cov.: 33 AF XY: 0.100 AC XY: 7449 AN XY: 74370

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.0625

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.0243

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.00860

Gnomad4 OTH AF: 0.0665

Alfa AF: 0.0245 Hom.: 480

Bravo AF: 0.115

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	1.2
DANN	Benign	0.60

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: rs11829037; hg19: chr12-121151093;