chr18-50801445-G-T

Variant names:

• chr18-50801445-G-T
• NM_031939.6:c.489C>A
• MRO p.Ala163Ala

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_031939.6(MRO):​c.489C>A​(p.Ala163Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 30)
• Consequence: MRO NM_031939.6 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 0 publications found

Genes affected

MRO (HGNC:24121): (maestro) This gene is specifically transcribed in males before and after differentiation of testis, and the encoded protein may play an important role in a mammalian sex determination. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BP7: Synonymous conserved (PhyloP=0.102 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031939.6. 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
	MRO	NM_031939.6	MANE Select	c.489C>A	p.Ala163Ala	synonymous	Exon 6 of 8	NP_114145.2	Q9BYG7-1
	MRO	NM_001127176.3		c.531C>A	p.Ala177Ala	synonymous	Exon 5 of 7	NP_001120648.1	Q9BYG7-5
	MRO	NM_001369508.2		c.489C>A	p.Ala163Ala	synonymous	Exon 6 of 8	NP_001356437.1	Q9BYG7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRO	ENST00000398439.8	TSL:1 MANE Select	c.489C>A	p.Ala163Ala	synonymous	Exon 6 of 8	ENSP00000381465.2	Q9BYG7-1
	MRO	ENST00000256425.6	TSL:1	c.489C>A	p.Ala163Ala	synonymous	Exon 6 of 8	ENSP00000256425.2	Q9BYG7-1
	MRO	ENST00000585524.5	TSL:1	n.*301C>A		non_coding_transcript_exon	Exon 6 of 8	ENSP00000465783.1	K7EKU2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 39

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	6.0
DANN	Benign	0.51
PhyloP100		0.10

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr18-48327815;