rs11167061

Positions:

• chr8-141447594-G-A

Variant summary

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

The ENST00000430863.5(MROH5):​c.2819+313C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 304,824 control chromosomes in the GnomAD database, including 5,401 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 (2394 hom., cov: 33)
  • Exomes 𝑓: 0.19 (3007 hom.)
• Consequence: MROH5 ENST00000430863.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

MROH5 (HGNC:42976): (maestro heat like repeat family member 5 (gene/pseudogene))

LOC105375789 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MROH5	NR_102363.3	n.2559+313C>T		intron_variant, non_coding_transcript_variant
LOC105375789	XR_928722.3	n.8120+481G>A		intron_variant, non_coding_transcript_variant
LOC124900270	XR_007061208.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MROH5	ENST00000430863.5	c.2819+313C>T		intron_variant		1		P5
MROH5	ENST00000521053.5	c.*2362+313C>T		intron_variant, NMD_transcript_variant		5		A2
MROH5	ENST00000523857.5	c.*2630+313C>T		intron_variant, NMD_transcript_variant		2		A2
	ENST00000458800.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23933 AN: 152110 Hom.: 2393 Cov.: 33

Gnomad AFR AF: 0.0417

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.188 AC: 28634 AN: 152596 Hom.: 3007 Cov.: 0 AF XY: 0.187 AC XY: 14402 AN XY: 77086

Gnomad4 AFR exome AF: 0.0407

Gnomad4 AMR exome AF: 0.122

Gnomad4 ASJ exome AF: 0.276

Gnomad4 EAS exome AF: 0.237

Gnomad4 SAS exome AF: 0.102

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.184

GnomAD4 genome AF: 0.157 AC: 23940 AN: 152228 Hom.: 2394 Cov.: 33 AF XY: 0.151 AC XY: 11217 AN XY: 74420

Gnomad4 AFR AF: 0.0417

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.184

Alfa AF: 0.177 Hom.: 522

Bravo AF: 0.154

Asia WGS AF: 0.167 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.78

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: rs11167061; hg19: chr8-142457694;