rs2839698

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001400176.1(MRPL23):​c.498-13918G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Consequence

MRPL23
NM_001400176.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.461
Variant links:
Genes affected
H19 (HGNC:4713): (H19 imprinted maternally expressed transcript) This gene is located in an imprinted region of chromosome 11 near the insulin-like growth factor 2 (IGF2) gene. This gene is only expressed from the maternally-inherited chromosome, whereas IGF2 is only expressed from the paternally-inherited chromosome. The product of this gene is a long non-coding RNA which functions as a tumor suppressor. Mutations in this gene have been associated with Beckwith-Wiedemann Syndrome and Wilms tumorigenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
MRPL23 (HGNC:10322): (mitochondrial ribosomal protein L23) Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein. The gene is biallelically expressed, despite its location within a region of imprinted genes on chromosome 11. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MRPL23NM_001400176.1 linkc.498-13918G>A intron_variant Intron 5 of 6 NP_001387105.1
MRPL23XM_011520273.2 linkc.498-13918G>A intron_variant Intron 5 of 6 XP_011518575.1
H19NR_002196.3 linkn.220C>T non_coding_transcript_exon_variant Exon 1 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
H19ENST00000412788.6 linkn.220C>T non_coding_transcript_exon_variant Exon 1 of 5 1
H19ENST00000414790.9 linkn.221C>T non_coding_transcript_exon_variant Exon 1 of 5 1
H19ENST00000411861.6 linkn.220C>T non_coding_transcript_exon_variant Exon 1 of 4 2

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD3 exomes
AF:
0.411
AC:
53912
AN:
131236
Hom.:
11985
AF XY:
0.411
AC XY:
29382
AN XY:
71544
show subpopulations
Gnomad AFR exome
AF:
0.101
Gnomad AMR exome
AF:
0.378
Gnomad ASJ exome
AF:
0.502
Gnomad EAS exome
AF:
0.316
Gnomad SAS exome
AF:
0.294
Gnomad FIN exome
AF:
0.537
Gnomad NFE exome
AF:
0.505
Gnomad OTH exome
AF:
0.446
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.459
Hom.:
4573
Asia WGS
AF:
0.276
AC:
959
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
3.9
DANN
Benign
0.44

Splicing

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: rs2839698; hg19: chr11-2018853; COSMIC: COSV66403896; API