rs2849239

Positions:

• chr18-50818472-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MRO	NM_031939.6	c.-5+1109C>T		intron_variant		ENST00000398439.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRO	ENST00000398439.8	c.-5+1109C>T		intron_variant		1	NM_031939.6	P1

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

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0811

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.135

Alfa AF: 0.186 Hom.: 349

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

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

Other links and lift over

dbSNP: rs2849239; hg19: chr18-48344842;