9-137077761-G-T

Variant names:

• chr9-137077761-G-T
• NM_207309.3:c.229G>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_207309.3(UAP1L1):​c.229G>T​(p.Glu77*) variant causes a stop gained change. The variant allele was found at a frequency of 0.000000898 in 1,113,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 9.0e-7 (0 hom.)
• Consequence: UAP1L1 NM_207309.3 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.10

Genes affected

UAP1L1 (HGNC:28082): (UDP-N-acetylglucosamine pyrophosphorylase 1 like 1) Predicted to enable UDP-N-acetylglucosamine diphosphorylase activity. Predicted to be involved in UDP-N-acetylglucosamine biosynthetic process. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UAP1L1	NM_207309.3	c.229G>T	p.Glu77*	stop_gained	Exon 1 of 9	ENST00000409858.8	NP_997192.2
UAP1L1	XM_047424066.1	c.229G>T	p.Glu77*	stop_gained	Exon 1 of 8		XP_047280022.1
UAP1L1	XM_006717317.4	c.229G>T	p.Glu77*	stop_gained	Exon 1 of 8		XP_006717380.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UAP1L1	ENST00000409858.8	c.229G>T	p.Glu77*	stop_gained	Exon 1 of 9	1	NM_207309.3	ENSP00000386935.3
UAP1L1	ENST00000476184.5	n.229G>T		non_coding_transcript_exon_variant	Exon 1 of 3	3		ENSP00000484649.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 8.98e-7 AC: 1 AN: 1113020 Hom.: 0 Cov.: 31 AF XY: 0.00000188 AC XY: 1 AN XY: 530874

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000311

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Uncertain	0.10
CADD	Pathogenic	36
DANN	Uncertain	0.98
Eigen	Benign	0.070
Eigen_PC	Benign	-0.26
FATHMM_MKL	Benign	0.73	D
Vest4		0.034
GERP RS		0.64

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-139972213;