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GeneBe

11-1952119-G-A

Variant summary

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

The NM_021134.4(MRPL23):c.141-8G>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 0.0 ( 0 hom., cov: 2)
Exomes 𝑓: 0.0029 ( 6 hom. )
Failed GnomAD Quality Control

Consequence

MRPL23
NM_021134.4 splice_region, splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.00008258
2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.649

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=-0.82).
BP6
?
Variant 11-1952119-G-A is Benign according to our data. Variant chr11-1952119-G-A is described in ClinVar as [Benign]. Clinvar id is 791542.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 6 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MRPL23NM_021134.4 linkuse as main transcriptc.141-8G>A splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000397298.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MRPL23ENST00000397298.8 linkuse as main transcriptc.141-8G>A splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_021134.4 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
8
AN:
17540
Hom.:
0
Cov.:
2
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.0159
Gnomad AMR
AF:
0.00101
Gnomad ASJ
AF:
0.00181
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000319
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00289
AC:
727
AN:
251328
Hom.:
6
AF XY:
0.00295
AC XY:
401
AN XY:
135892
show subpopulations
Gnomad AFR exome
AF:
0.000862
Gnomad AMR exome
AF:
0.00437
Gnomad ASJ exome
AF:
0.0129
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00232
Gnomad FIN exome
AF:
0.000508
Gnomad NFE exome
AF:
0.00267
Gnomad OTH exome
AF:
0.00767
GnomAD4 exome
AF:
0.000277
AC:
27
AN:
97538
Hom.:
0
AF XY:
0.000271
AC XY:
14
AN XY:
51684
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000309
Gnomad4 ASJ exome
AF:
0.00142
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000222
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000215
Gnomad4 OTH exome
AF:
0.000555
Alfa
AF:
0.00300
Hom.:
1
Asia WGS
AF:
0.00202
AC:
7
AN:
3478
EpiCase
AF:
0.00382
EpiControl
AF:
0.00397

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 12, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
0.19
Dann
Benign
0.73

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000083
dbscSNV1_RF
Benign
0.014
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: rs117034794; hg19: chr11-1973349; API