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GeneBe

19-49490776-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_012423.4(RPL13A):c.257-3C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00251 in 152254 control chromosomes in the gnomAD Genomes database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0025 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00063 ( 1 hom. )

Consequence

RPL13A
NM_012423.4 splice_region, splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.002338
2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.268

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant 19-49490776-C-T is Benign according to our data. Variant chr19-49490776-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 715747.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 382 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPL13ANM_012423.4 linkuse as main transcriptc.257-3C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000391857.9
RPL13ANM_001270491.2 linkuse as main transcriptc.74-3C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
RPL13ANR_073024.2 linkuse as main transcriptn.269-3C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPL13AENST00000391857.9 linkuse as main transcriptc.257-3C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_012423.4 P1

Frequencies

GnomAD3 genomes
AF:
0.00251
AC:
382
AN:
152254
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00885
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.000633
AC:
159
AN:
251144
Hom.:
1
AF XY:
0.000449
AC XY:
61
AN XY:
135814
show subpopulations
Gnomad AFR exome
AF:
0.00837
Gnomad AMR exome
AF:
0.000521
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000264
Gnomad OTH exome
AF:
0.000326
GnomAD4 exome
AF:
0.000216
AC:
316
AN:
1461814
Hom.:
3
AF XY:
0.000191
AC XY:
139
AN XY:
727212
show subpopulations
Gnomad4 AFR exome
AF:
0.00753
Gnomad4 AMR exome
AF:
0.000604
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000180
Gnomad4 OTH exome
AF:
0.000281
Alfa
AF:
0.00146
Hom.:
2
Bravo
AF:
0.00300
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeJan 30, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
Cadd
Benign
5.9
Dann
Benign
0.68

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.0023
dbscSNV1_RF
Benign
0.092
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: rs112644132; hg19: chr19-49994033; API