ENST00000430863.5:c.2637+658G>A

Variant names:

• chr8-141448932-C-T
• rs11167062
• ENST00000430863.5:c.2637+658G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000430863.5(MROH5):​c.2637+658G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,952 control chromosomes in the GnomAD database, including 6,986 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 0.30 (6986 hom., cov: 32)
• Consequence: MROH5 ENST00000430863.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.323 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.2377+658G>A		intron	N/A
	MROH5	NR_102364.3		n.2648+658G>A		intron	N/A
	MROH5	NR_160399.1		n.2717+658G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH5	ENST00000430863.5	TSL:1	c.2637+658G>A		intron	N/A	ENSP00000431031.1
	MROH5	ENST00000521053.5	TSL:5	n.*2180+658G>A		intron	N/A	ENSP00000429433.1
	MROH5	ENST00000523857.5	TSL:2	n.*2448+658G>A		intron	N/A	ENSP00000427945.1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45667 AN: 151832 Hom.: 6985 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.326

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.301 AC: 45692 AN: 151952 Hom.: 6986 Cov.: 32 AF XY: 0.293 AC XY: 21778 AN XY: 74268

African (AFR) AF: 0.288 AC: 11950 AN: 41468

American (AMR) AF: 0.242 AC: 3700 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1538 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1664 AN: 5140

South Asian (SAS) AF: 0.189 AC: 914 AN: 4826

European-Finnish (FIN) AF: 0.253 AC: 2674 AN: 10576

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22179 AN: 67874

Other (OTH) AF: 0.329 AC: 692 AN: 2106

Alfa AF: 0.323 Hom.: 12848

Bravo AF: 0.303

Asia WGS AF: 0.285 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.55
PhyloP100		0.16

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: rs11167062; hg19: chr8-142459032; COSMIC: COSV71300843; COSMIC: COSV71300843;