rs2255672

Variant names:

• chr18-50806997-T-A
• rs2255672
• NM_031939.6:c.100-147A>T

Your query was ambiguous. Multiple possible variants found:

• chr18-50806997-T-A
• chr18-50806997-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_031939.6(MRO):​c.100-147A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000162 in 618,072 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 31)
  • Exomes 𝑓: 0.0000016 (0 hom.)
• Consequence: MRO NM_031939.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRO	NM_031939.6	c.100-147A>T		intron_variant	Intron 3 of 7	ENST00000398439.8	NP_114145.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRO	ENST00000398439.8	c.100-147A>T		intron_variant	Intron 3 of 7	1	NM_031939.6	ENSP00000381465.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000162 AC: 1 AN: 618072 Hom.: 0 AF XY: 0.00000310 AC XY: 1 AN XY: 322874

African (AFR) AF: 0.00 AC: 0 AN: 16012

American (AMR) AF: 0.00 AC: 0 AN: 21966

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15246

East Asian (EAS) AF: 0.00 AC: 0 AN: 33790

South Asian (SAS) AF: 0.00 AC: 0 AN: 50822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33996

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2704

European-Non Finnish (NFE) AF: 0.00000243 AC: 1 AN: 411780

Other (OTH) AF: 0.00 AC: 0 AN: 31756

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.7
DANN	Benign	0.83
PhyloP100		-0.18

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: rs2255672; hg19: chr18-48333367;