1-54691208-G-A

Variant names:

• chr1-54691208-G-A
• rs6588528
• NM_001039464.4:c.2712-1216G>A

Variant summary

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

The NM_001039464.4(MROH7):​c.2712-1216G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,060 control chromosomes in the GnomAD database, including 3,867 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 0.22 (3867 hom., cov: 32)
• Consequence: MROH7 NM_001039464.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321
• Publications: 1 publications found

Genes affected

MROH7 (HGNC:24802): (maestro heat like repeat family member 7) Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

MROH7-TTC4 (HGNC:49180): (MROH7-TTC4 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring MROH7 (maestro heat-like repeat family member 7) and TTC4 (tetratricopeptide repeat domain 4) genes. Alternative splicing results in multiple transcript variants, which are candidates for nonsense-mediated mRNA decay (NMD) and are unlikely to produce protein products. [provided by RefSeq, Aug 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MROH7	NM_001039464.4	c.2712-1216G>A		intron_variant	Intron 15 of 23	ENST00000421030.7	NP_001034553.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MROH7	ENST00000421030.7	c.2712-1216G>A		intron_variant	Intron 15 of 23	2	NM_001039464.4	ENSP00000396622.2
MROH7-TTC4	ENST00000414150.6	n.2712-1216G>A		intron_variant	Intron 15 of 32	2		ENSP00000410192.2

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32885 AN: 151942 Hom.: 3849 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.217 AC: 32924 AN: 152060 Hom.: 3867 Cov.: 32 AF XY: 0.217 AC XY: 16166 AN XY: 74360

African (AFR) AF: 0.282 AC: 11668 AN: 41446

American (AMR) AF: 0.292 AC: 4462 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1447 AN: 5162

South Asian (SAS) AF: 0.154 AC: 743 AN: 4814

European-Finnish (FIN) AF: 0.169 AC: 1790 AN: 10586

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11395 AN: 67998

Other (OTH) AF: 0.233 AC: 493 AN: 2114

Alfa AF: 0.185 Hom.: 11927

Bravo AF: 0.230

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.76
DANN	Benign	0.31
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism (auto)

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: rs6588528; hg19: chr1-55156881;