1-54222843-T-C

Variant names:

• chr1-54222843-T-C
• rs642990
• NM_001330602.1:c.1195-2282T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001330602.1(MRPL37):​c.1195-2282T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,128 control chromosomes in the GnomAD database, including 33,591 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 0.66 (33591 hom., cov: 33)
• Consequence: MRPL37 NM_001330602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 8 publications found

Genes affected

MRPL37 (HGNC:14034): (mitochondrial ribosomal protein L37) 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. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330602.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPL37	NM_001330602.1		c.1195-2282T>C		intron	N/A	NP_001317531.1	S4R369

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPL37	ENST00000605337.5	TSL:5	c.1195-2282T>C		intron	N/A	ENSP00000473980.1	S4R369

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99795 AN: 152010 Hom.: 33547 Cov.: 33

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.586

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.657 AC: 99899 AN: 152128 Hom.: 33591 Cov.: 33 AF XY: 0.659 AC XY: 49023 AN XY: 74372

African (AFR) AF: 0.794 AC: 32948 AN: 41506

American (AMR) AF: 0.646 AC: 9879 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1781 AN: 3466

East Asian (EAS) AF: 0.767 AC: 3954 AN: 5156

South Asian (SAS) AF: 0.701 AC: 3379 AN: 4822

European-Finnish (FIN) AF: 0.629 AC: 6665 AN: 10590

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39389 AN: 67980

Other (OTH) AF: 0.585 AC: 1235 AN: 2110

Alfa AF: 0.597 Hom.: 85055

Bravo AF: 0.661

Asia WGS AF: 0.744 AC: 2587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.9
DANN	Benign	0.53
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs642990; hg19: chr1-54688516;