rs958075

Variant summary

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

The ENST00000304788.4(NANP):​c.*1438C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,756 control chromosomes in the GnomAD database, including 10,888 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 0.36 ( 10888 hom., cov: 32)
Failed GnomAD Quality Control

Consequence

NANP
ENST00000304788.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0120
Variant links:
Genes affected
NANP (HGNC:16140): (N-acetylneuraminic acid phosphatase) Enables N-acylneuraminate-9-phosphatase activity. Involved in N-acetylneuraminate biosynthetic process. Predicted to be located in cytosol. [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=-0.9).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NANPNM_152667.3 linkuse as main transcriptc.*1438C>T 3_prime_UTR_variant 2/2 ENST00000304788.4 NP_689880.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NANPENST00000304788.4 linkuse as main transcriptc.*1438C>T 3_prime_UTR_variant 2/21 NM_152667.3 ENSP00000302441 P1

Frequencies

GnomAD3 genomes
AF:
0.362
AC:
54948
AN:
151640
Hom.:
10882
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.241
Gnomad AMI
AF:
0.300
Gnomad AMR
AF:
0.464
Gnomad ASJ
AF:
0.578
Gnomad EAS
AF:
0.0164
Gnomad SAS
AF:
0.450
Gnomad FIN
AF:
0.386
Gnomad MID
AF:
0.417
Gnomad NFE
AF:
0.418
Gnomad OTH
AF:
0.400
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.362
AC:
54967
AN:
151756
Hom.:
10888
Cov.:
32
AF XY:
0.362
AC XY:
26803
AN XY:
74142
show subpopulations
Gnomad4 AFR
AF:
0.241
Gnomad4 AMR
AF:
0.464
Gnomad4 ASJ
AF:
0.578
Gnomad4 EAS
AF:
0.0157
Gnomad4 SAS
AF:
0.450
Gnomad4 FIN
AF:
0.386
Gnomad4 NFE
AF:
0.418
Gnomad4 OTH
AF:
0.399
Alfa
AF:
0.398
Hom.:
3722
Bravo
AF:
0.361
Asia WGS
AF:
0.229
AC:
797
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
5.0
DANN
Benign
0.68

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

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

Other links and lift over

dbSNP: rs958075; hg19: chr20-25595123; API