18-50796023-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031939.6(MRO):c.*3314C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,168 control chromosomes in the GnomAD database, including 3,225 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 0.16 (3225 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MRO NM_031939.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRO	NM_031939.6	c.*3314C>A		3_prime_UTR_variant	8/8	ENST00000398439.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRO	ENST00000398439.8	c.*3314C>A		3_prime_UTR_variant	8/8	1	NM_031939.6	P1
MRO	ENST00000256425.6	c.*3314C>A		3_prime_UTR_variant	8/8	1		P1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24772 AN: 152050 Hom.: 3214 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.147

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.163 AC: 24831 AN: 152168 Hom.: 3225 Cov.: 32 AF XY: 0.163 AC XY: 12144 AN XY: 74390

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0679

Gnomad4 OTH AF: 0.151

Alfa AF: 0.0326 Hom.: 23

Bravo AF: 0.181

Asia WGS AF: 0.198 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.2
Dann	Benign	0.61

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: rs8094063; hg19: chr18-48322393;