1-162576990-C-T

Variant names:

• chr1-162576990-C-T
• rs6700714
• NM_001324116.5:c.485+9C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001324116.5(UAP1):​c.485+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00428 in 1,612,214 control chromosomes in the GnomAD database, including 244 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.022 (128 hom., cov: 31)
  • Exomes 𝑓: 0.0024 (116 hom.)
• Consequence: UAP1 NM_001324116.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -3.07
• Publications: 1 publications found

Genes affected

UAP1 (HGNC:12457): (UDP-N-acetylglucosamine pyrophosphorylase 1) Enables identical protein binding activity. Predicted to be involved in UDP-N-acetylglucosamine biosynthetic process. Located in cytosol; nucleoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 1-162576990-C-T is Benign according to our data. Variant chr1-162576990-C-T is described in ClinVar as [Benign]. Clinvar id is 772818.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.073 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UAP1	NM_001324116.5	c.485+9C>T		intron_variant	Intron 3 of 10	ENST00000367925.6	NP_001311045.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UAP1	ENST00000367925.6	c.485+9C>T		intron_variant	Intron 3 of 10	5	NM_001324116.5	ENSP00000356902.1
UAP1	ENST00000367926.9	c.485+9C>T		intron_variant	Intron 3 of 9	1		ENSP00000356903.4

Frequencies

GnomAD3 genomes AF: 0.0218 AC: 3312 AN: 152062 Hom.: 128 Cov.: 31

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00773

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0000944

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000485

Gnomad OTH AF: 0.0182

GnomAD2 exomes AF: 0.00588 AC: 1476 AN: 250954 AF XY: 0.00432

Gnomad AFR exome AF: 0.0783

Gnomad AMR exome AF: 0.00399

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000353

Gnomad OTH exome AF: 0.00278

GnomAD4 exome AF: 0.00245 AC: 3572 AN: 1460034 Hom.: 116 Cov.: 30 AF XY: 0.00212 AC XY: 1538 AN XY: 726464

African (AFR) AF: 0.0799 AC: 2671 AN: 33424

American (AMR) AF: 0.00450 AC: 201 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26128

East Asian (EAS) AF: 0.00 AC: 0 AN: 39694

South Asian (SAS) AF: 0.000360 AC: 31 AN: 86218

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53414

Middle Eastern (MID) AF: 0.00716 AC: 41 AN: 5726

European-Non Finnish (NFE) AF: 0.000264 AC: 293 AN: 1110392

Other (OTH) AF: 0.00555 AC: 335 AN: 60324

GnomAD4 genome AF: 0.0218 AC: 3322 AN: 152180 Hom.: 128 Cov.: 31 AF XY: 0.0211 AC XY: 1568 AN XY: 74398

African (AFR) AF: 0.0752 AC: 3120 AN: 41504

American (AMR) AF: 0.00772 AC: 118 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00187 AC: 9 AN: 4822

European-Finnish (FIN) AF: 0.0000944 AC: 1 AN: 10590

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000485 AC: 33 AN: 68012

Other (OTH) AF: 0.0180 AC: 38 AN: 2114

Alfa AF: 0.00936 Hom.: 43

Bravo AF: 0.0242

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.010
DANN	Benign	0.63
PhyloP100		-3.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs6700714; hg19: chr1-162546780;