rs11777747

Positions:

• chr8-141456721-C-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899

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=-0.96).
• 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: 19174 AN: 151934 Hom.: 1536 Cov.: 32

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.126 AC: 19184 AN: 152052 Hom.: 1537 Cov.: 32 AF XY: 0.121 AC XY: 9000 AN XY: 74306

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.159

Alfa AF: 0.174 Hom.: 4028

Bravo AF: 0.121

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.87
DANN	Benign	0.56

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: rs11777747; hg19: chr8-142466821;