rs11777747
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000430863.5(MROH5):c.2478-6972G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,052 control chromosomes in the GnomAD database, including 1,537 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 0.13 ( 1537 hom., cov: 32)
Consequence
MROH5
ENST00000430863.5 intron
ENST00000430863.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.899
Genes affected
MROH5 (HGNC:42976): (maestro heat like repeat family member 5 (gene/pseudogene))
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MROH5 | NR_102363.3 | n.2218-6972G>A | intron_variant, non_coding_transcript_variant | ||||
LOC105375789 | XR_928722.3 | n.8229+1978C>T | intron_variant, non_coding_transcript_variant | ||||
MROH5 | NR_102364.3 | n.2489-6972G>A | intron_variant, non_coding_transcript_variant | ||||
MROH5 | NR_160399.1 | n.2558-6972G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MROH5 | ENST00000430863.5 | c.2478-6972G>A | intron_variant | 1 | P5 | ||||
MROH5 | ENST00000521053.5 | c.*2021-6972G>A | intron_variant, NMD_transcript_variant | 5 | A2 | ||||
MROH5 | ENST00000523857.5 | c.*2289-6972G>A | intron_variant, NMD_transcript_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.126 AC: 19174AN: 151934Hom.: 1536 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
19174
AN:
151934
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.126 AC: 19184AN: 152052Hom.: 1537 Cov.: 32 AF XY: 0.121 AC XY: 9000AN XY: 74306
GnomAD4 genome
?
AF:
AC:
19184
AN:
152052
Hom.:
Cov.:
32
AF XY:
AC XY:
9000
AN XY:
74306
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
504
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at