rs4628973

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_027335.2(URAHP):​n.228+1139T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,320 control chromosomes in the GnomAD database, including 18,370 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 0.46 ( 18370 hom., cov: 31)

Consequence

URAHP
NR_027335.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.91
Variant links:
Genes affected
URAHP (HGNC:43695): (urate (hydroxyiso-) hydrolase, pseudogene) Predicted to enable hydroxyisourate hydrolase activity. Predicted to be involved in allantoin metabolic process; purine-containing compound catabolic process; and urate catabolic process. Predicted to be active in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
URAHPNR_027335.2 linkuse as main transcriptn.228+1139T>C intron_variant, non_coding_transcript_variant
URAHPNR_027336.2 linkuse as main transcriptn.181+1139T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
URAHPENST00000409873.5 linkuse as main transcriptn.228+1139T>C intron_variant, non_coding_transcript_variant 1
URAHPENST00000517889.5 linkuse as main transcriptn.171+1139T>C intron_variant, non_coding_transcript_variant 1
URAHPENST00000610227.1 linkuse as main transcriptn.200+1139T>C intron_variant, non_coding_transcript_variant
URAHPENST00000521551.5 linkuse as main transcriptn.234+1139T>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.455
AC:
68841
AN:
151202
Hom.:
18316
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.705
Gnomad AMI
AF:
0.200
Gnomad AMR
AF:
0.471
Gnomad ASJ
AF:
0.250
Gnomad EAS
AF:
0.792
Gnomad SAS
AF:
0.390
Gnomad FIN
AF:
0.495
Gnomad MID
AF:
0.214
Gnomad NFE
AF:
0.291
Gnomad OTH
AF:
0.372
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.456
AC:
68955
AN:
151320
Hom.:
18370
Cov.:
31
AF XY:
0.464
AC XY:
34334
AN XY:
73920
show subpopulations
Gnomad4 AFR
AF:
0.705
Gnomad4 AMR
AF:
0.472
Gnomad4 ASJ
AF:
0.250
Gnomad4 EAS
AF:
0.792
Gnomad4 SAS
AF:
0.388
Gnomad4 FIN
AF:
0.495
Gnomad4 NFE
AF:
0.291
Gnomad4 OTH
AF:
0.370
Alfa
AF:
0.370
Hom.:
2629
Bravo
AF:
0.470
Asia WGS
AF:
0.600
AC:
2089
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.80
DANN
Benign
0.095

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4628973; hg19: chr16-90112226; COSMIC: COSV51946484; API