rs1263891239

Variant names:

• chr8-143567456-C-A
• rs1263891239
• NM_001100878.2:c.1943G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-143567456-C-A
• chr8-143567456-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001100878.2(MROH6):​c.1943G>T​(p.Arg648Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R648Q) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 36)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MROH6 NM_001100878.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 1 publications found

Genes affected

MROH6 (HGNC:27814): (maestro heat like repeat family member 6)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10695481).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MROH6	NM_001100878.2	c.1943G>T	p.Arg648Leu	missense_variant	Exon 14 of 14	ENST00000398882.8	NP_001094348.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MROH6	ENST00000398882.8	c.1943G>T	p.Arg648Leu	missense_variant	Exon 14 of 14	5	NM_001100878.2	ENSP00000381857.3

Frequencies

GnomAD3 genomes Cov.: 36

GnomAD2 exomes AF: 0.00 AC: 0 AN: 37894 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1227058 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 592880

African (AFR) AF: 0.00 AC: 0 AN: 25166

American (AMR) AF: 0.00 AC: 0 AN: 13892

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17142

East Asian (EAS) AF: 0.00 AC: 0 AN: 29466

South Asian (SAS) AF: 0.00 AC: 0 AN: 54674

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38510

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3356

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 995004

Other (OTH) AF: 0.00 AC: 0 AN: 49848

GnomAD4 genome Cov.: 36

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.073
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.65
CADD	Benign	3.0
DANN	Benign	0.96
DEOGEN2	Benign	0.0035	T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.14	N
M_CAP	Benign	0.037	D
MetaRNN	Benign	0.11	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	N
PhyloP100		-0.43
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-1.3	N
REVEL	Benign	0.022
Sift	Benign	0.15	T
Sift4G	Uncertain	0.048	D
Polyphen		0.0010	B
Vest4		0.15
MutPred		0.41		Loss of disorder (P = 0.0576);
MVP		0.014
MPC		0.018
ClinPred		0.061	T
GERP RS		-0.68
Varity_R		0.041
gMVP		0.11
Mutation Taster		=94/6	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs1263891239; hg19: chr8-144649626;