Menu
GeneBe

19-49491421-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_012423.4(RPL13A):c.403-4G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. 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 Benign (★).

Frequency

Genomes: 𝑓 0.033 ( 20 hom., cov: 0)
Exomes 𝑓: 0.019 ( 13 hom. )

Consequence

RPL13A
NM_012423.4 splice_region, splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.00002410
2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.55

Links

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=-0.86).
BP6
?
Variant 19-49491421-G-A is Benign according to our data. Variant chr19-49491421-G-A is described in ClinVar as [Benign]. Clinvar id is 775419.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-49491421-G-A is described in Lovd as [Likely_benign].
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0983 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPL13ANM_012423.4 linkuse as main transcriptc.403-4G>A splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000391857.9
RPL13ANM_001270491.2 linkuse as main transcriptc.220-4G>A splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
RPL13ANR_073024.2 linkuse as main transcriptn.415-4G>A 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.403-4G>A splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_012423.4 P1

Frequencies

GnomAD3 genomes
AF:
0.0330
AC:
517
AN:
15690
Hom.:
20
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.106
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0152
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000380
Gnomad OTH
AF:
0.0135
GnomAD3 exomes
AF:
0.0188
AC:
391
AN:
20758
Hom.:
13
AF XY:
0.0155
AC XY:
172
AN XY:
11118
show subpopulations
Gnomad AFR exome
AF:
0.173
Gnomad AMR exome
AF:
0.0126
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000336
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00127
Gnomad OTH exome
AF:
0.0141
GnomAD4 exome
AF:
0.00859
AC:
1439
AN:
167502
Hom.:
53
AF XY:
0.00759
AC XY:
640
AN XY:
84290
show subpopulations
Gnomad4 AFR exome
AF:
0.164
Gnomad4 AMR exome
AF:
0.0106
Gnomad4 ASJ exome
AF:
0.000244
Gnomad4 EAS exome
AF:
0.000250
Gnomad4 SAS exome
AF:
0.000675
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000309
Gnomad4 OTH exome
AF:
0.0169

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 testingInvitaeJun 05, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
0.051
Dann
Benign
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000024
dbscSNV1_RF
Benign
0.0
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: rs115924751; hg19: chr19-49994678; API