rs2849239

Variant names:

• chr18-50818472-G-A
• rs2849239
• NM_031939.6:c.-5+1109C>T

Variant summary

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

The NM_031939.6(MRO):​c.-5+1109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,138 control chromosomes in the GnomAD database, including 2,323 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 0.17 (2323 hom., cov: 32)
• Consequence: MRO NM_031939.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 1 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRO	NM_031939.6	c.-5+1109C>T		intron_variant	Intron 2 of 7	ENST00000398439.8	NP_114145.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRO	ENST00000398439.8	c.-5+1109C>T		intron_variant	Intron 2 of 7	1	NM_031939.6	ENSP00000381465.2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25202 AN: 152018 Hom.: 2316 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0810

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.166 AC: 25231 AN: 152138 Hom.: 2323 Cov.: 32 AF XY: 0.162 AC XY: 12072 AN XY: 74348

African (AFR) AF: 0.126 AC: 5231 AN: 41522

American (AMR) AF: 0.101 AC: 1543 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3470

East Asian (EAS) AF: 0.0811 AC: 419 AN: 5166

South Asian (SAS) AF: 0.168 AC: 806 AN: 4810

European-Finnish (FIN) AF: 0.215 AC: 2273 AN: 10568

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14013 AN: 68002

Other (OTH) AF: 0.135 AC: 285 AN: 2114

Alfa AF: 0.183 Hom.: 352

Bravo AF: 0.152

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.72
PhyloP100		0.062
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2849239; hg19: chr18-48344842;