rs11167061

Variant names:

• chr8-141447594-G-A
• rs11167061
• ENST00000430863.5:c.2819+313C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

LOC105375789 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430863.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH5	NR_102363.3		n.2559+313C>T		intron	N/A
	MROH5	NR_102364.3		n.2830+313C>T		intron	N/A
	MROH5	NR_160399.1		n.2899+313C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH5	ENST00000430863.5	TSL:1	c.2819+313C>T		intron	N/A	ENSP00000431031.1
	MROH5	ENST00000521053.5	TSL:5	n.*2362+313C>T		intron	N/A	ENSP00000429433.1
	MROH5	ENST00000523857.5	TSL:2	n.*2630+313C>T		intron	N/A	ENSP00000427945.1

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

African (AFR) AF: 0.0407 AC: 197 AN: 4836

American (AMR) AF: 0.122 AC: 586 AN: 4786

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 1551 AN: 5626

East Asian (EAS) AF: 0.237 AC: 2395 AN: 10120

South Asian (SAS) AF: 0.102 AC: 717 AN: 7062

European-Finnish (FIN) AF: 0.137 AC: 1420 AN: 10342

Middle Eastern (MID) AF: 0.178 AC: 150 AN: 842

European-Non Finnish (NFE) AF: 0.200 AC: 19682 AN: 98472

Other (OTH) AF: 0.184 AC: 1936 AN: 10510

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

African (AFR) AF: 0.0417 AC: 1732 AN: 41570

American (AMR) AF: 0.138 AC: 2117 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1126 AN: 3468

East Asian (EAS) AF: 0.175 AC: 907 AN: 5174

South Asian (SAS) AF: 0.136 AC: 655 AN: 4822

European-Finnish (FIN) AF: 0.145 AC: 1535 AN: 10594

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15232 AN: 67982

Other (OTH) AF: 0.184 AC: 388 AN: 2112

Alfa AF: 0.184 Hom.: 1049

Bravo AF: 0.154

Asia WGS AF: 0.167 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.78
PhyloP100		-1.5

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: rs11167061; hg19: chr8-142457694;