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GeneBe

rs5275

Variant summary

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

The NM_000963.4(PTGS2):c.*427T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151922 control chromosomes in the gnomAD Genomes database, including 13726 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as other (no stars).

Frequency

Genomes: đť‘“ 0.40 ( 13726 hom., cov: 33)

Consequence

PTGS2
NM_000963.4 3_prime_UTR

Scores

2

Clinical Significance

other no assertion criteria provided O:1

Conservation

PhyloP100: -1.15

Links

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
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTGS2NM_000963.4 linkuse as main transcriptc.*427T>C 3_prime_UTR_variant 10/10 ENST00000367468.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTGS2ENST00000367468.10 linkuse as main transcriptc.*427T>C 3_prime_UTR_variant 10/101 NM_000963.4 P1
PTGS2ENST00000490885.6 linkuse as main transcriptn.2657T>C non_coding_transcript_exon_variant 9/91
PTGS2ENST00000680451.1 linkuse as main transcriptc.*427T>C 3_prime_UTR_variant 11/11 P1
PTGS2ENST00000681605.1 linkuse as main transcriptc.*1914T>C 3_prime_UTR_variant, NMD_transcript_variant 10/10

Frequencies

GnomAD3 genomes
AF:
0.404
AC:
61413
AN:
151922
Hom.:
13726
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.607
Gnomad AMI
AF:
0.238
Gnomad AMR
AF:
0.319
Gnomad ASJ
AF:
0.336
Gnomad EAS
AF:
0.192
Gnomad SAS
AF:
0.391
Gnomad FIN
AF:
0.296
Gnomad MID
AF:
0.287
Gnomad NFE
AF:
0.341
Gnomad OTH
AF:
0.365
GnomAD4 exome
AF:
0.347
AC:
127
AN:
366
Hom.:
18
AF XY:
0.357
AC XY:
80
AN XY:
224
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.500
Gnomad4 ASJ exome
AF:
0.500
Gnomad4 EAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.341
Gnomad4 NFE exome
AF:
0.405
Gnomad4 OTH exome
AF:
0.250
Alfa
AF:
0.350
Hom.:
13597
Bravo
AF:
0.412
Asia WGS
AF:
0.336
AC:
1165
AN:
3468

ClinVar

Significance: other
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Cholangiocarcinoma Other:1
other, no assertion criteria providedresearchDepartment of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin BerlinDec 10, 2022No association with disease-free or overall survival after resection of intrahepatic Cholangiocarcinoma No association with disease-free or overall survival

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
0.64
Dann
Benign
0.38

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: rs5275; hg19: chr1-186643058;