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GeneBe

19-55391634-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_000991.5(RPL28):c.*3302T>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 0.0029 in 1,546,214 control chromosomes in the GnomAD database, including 99 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 60 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 39 hom. )

Consequence

RPL28
NM_000991.5 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.903
Variant links:
Genes affected
RPL28 (HGNC:10330): (ribosomal protein L28) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L28E family of ribosomal proteins. It is located in the cytoplasm. Variable expression of this gene in colorectal cancers compared to adjacent normal tissues has been observed, although no correlation between the level of expression and the severity of the disease has been found. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Oct 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 19-55391634-T-C is Benign according to our data. Variant chr19-55391634-T-C is described in ClinVar as [Benign]. Clinvar id is 775430.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.015 (2278/152350) while in subpopulation AFR AF= 0.0514 (2136/41582). AF 95% confidence interval is 0.0496. There are 60 homozygotes in gnomad4. There are 1117 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2278 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPL28NM_000991.5 linkuse as main transcriptc.*3302T>C 3_prime_UTR_variant 5/5 ENST00000344063.7
RPL28NM_001136135.2 linkuse as main transcriptc.405T>C p.Cys135= synonymous_variant 5/5
RPL28NM_001136134.1 linkuse as main transcriptc.*3418T>C 3_prime_UTR_variant 4/4
RPL28NM_001363697.1 linkuse as main transcriptc.324+3586T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPL28ENST00000344063.7 linkuse as main transcriptc.*3302T>C 3_prime_UTR_variant 5/51 NM_000991.5 P1P46779-1
RPL28ENST00000426763.3 linkuse as main transcriptn.5154T>C non_coding_transcript_exon_variant 2/21
RPL28ENST00000558815.5 linkuse as main transcriptc.405T>C p.Cys135= synonymous_variant 5/52 P46779-3
RPL28ENST00000560055.5 linkuse as main transcriptc.324+3586T>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0149
AC:
2269
AN:
152232
Hom.:
58
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0513
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00576
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000353
Gnomad OTH
AF:
0.0139
GnomAD3 exomes
AF:
0.00370
AC:
561
AN:
151642
Hom.:
6
AF XY:
0.00278
AC XY:
224
AN XY:
80642
show subpopulations
Gnomad AFR exome
AF:
0.0552
Gnomad AMR exome
AF:
0.00365
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000176
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000297
Gnomad OTH exome
AF:
0.00301
GnomAD4 exome
AF:
0.00159
AC:
2211
AN:
1393864
Hom.:
39
Cov.:
27
AF XY:
0.00141
AC XY:
972
AN XY:
687660
show subpopulations
Gnomad4 AFR exome
AF:
0.0504
Gnomad4 AMR exome
AF:
0.00398
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000253
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000173
Gnomad4 OTH exome
AF:
0.00427
GnomAD4 genome
AF:
0.0150
AC:
2278
AN:
152350
Hom.:
60
Cov.:
33
AF XY:
0.0150
AC XY:
1117
AN XY:
74500
show subpopulations
Gnomad4 AFR
AF:
0.0514
Gnomad4 AMR
AF:
0.00562
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000353
Gnomad4 OTH
AF:
0.0137
Alfa
AF:
0.00654
Hom.:
19
Bravo
AF:
0.0168
Asia WGS
AF:
0.00346
AC:
12
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeApr 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.9
DANN
Benign
0.40

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: rs7260639; hg19: chr19-55903002; API