dbSNP rs3209: MRPL10:c.*448A>G (chr17-47823757-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145255.4(MRPL10):c.*448A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 211,732 control chromosomes in the GnomAD database, including 10,184 homozygotes. 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: 𝑓 0.27 ( 6956 hom., cov: 33)

Exomes 𝑓: 0.31 ( 3228 hom. )

Consequence

MRPL10
NM_145255.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32

Variant links:

Genes affected

MRPL10 (HGNC:14055): (mitochondrial ribosomal protein L10) 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. Sequence analysis identified three transcript variants that encode two different isoforms. A pseudogene corresponding to this gene is found on chromosome 5q. [provided by RefSeq, Nov 2010]

MRPL10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MRPL10	NM_145255.4 link	c.*448A>G	3_prime_UTR_variant	Exon 5 of 5	ENST00000351111.7	NP_660298.2	Q7Z7H8-1
MRPL10	NM_148887.3 link	c.*448A>G	3_prime_UTR_variant	Exon 6 of 6		NP_683685.1	Q7Z7H8-2
MRPL10	XM_024450575.2 link	c.*448A>G	3_prime_UTR_variant	Exon 6 of 6		XP_024306343.1
MRPL10	NR_037575.2 link	n.1413A>G	non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPL10	ENST00000351111 link	c.*448A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_145255.4	ENSP00000324100.4		Q7Z7H8-1

Frequencies

GnomAD3 genomes

AF:

0.272

AC:

41295

AN:

152084

Hom.:

6954

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.241

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.361

Gnomad EAS

AF:

0.0148

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.403

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.267

GnomAD4 exome

AF:

0.309

AC:

18380

AN:

59530

Hom.:

3228

Cov.:

AF XY:

0.294

AC XY:

9404

AN XY:

31974

show subpopulations

Gnomad4 AFR exome

AF:

0.0735

Gnomad4 AMR exome

AF:

0.216

Gnomad4 ASJ exome

AF:

0.323

Gnomad4 EAS exome

AF:

0.0124

Gnomad4 SAS exome

AF:

0.219

Gnomad4 FIN exome

AF:

0.396

Gnomad4 NFE exome

AF:

0.354

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.271

AC:

41314

AN:

152202

Hom.:

6956

Cov.:

AF XY:

0.270

AC XY:

20058

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.112

Gnomad4 AMR

AF:

0.219

Gnomad4 ASJ

AF:

0.361

Gnomad4 EAS

AF:

0.0149

Gnomad4 SAS

AF:

0.220

Gnomad4 FIN

AF:

0.403

Gnomad4 NFE

AF:

0.379

Gnomad4 OTH

AF:

0.265

Alfa

AF:

0.318

Hom.:

1394

Bravo

AF:

0.251

Asia WGS

AF:

0.122

AC:

424

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.10

DANN

Benign

0.51

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over