rs571199

chr1-54673945-G-A

Variant summary

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

The NM_001039464.4(MROH7):c.1801-71G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,568,000 control chromosomes in the GnomAD database, including 68,178 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 0.28 (6183 hom., cov: 32)
  • Exomes 𝑓: 0.29 (61995 hom.)
• Consequence: MROH7 NM_001039464.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MROH7	NM_001039464.4	c.1801-71G>A		intron_variant		ENST00000421030.7
MROH7-TTC4	NR_037639.2	n.2319-55G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MROH7	ENST00000421030.7	c.1801-71G>A		intron_variant		2	NM_001039464.4	P2

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42906 AN: 151992 Hom.: 6188 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.311

GnomAD4 exome AF: 0.293 AC: 414598 AN: 1415890 Hom.: 61995 Cov.: 25 AF XY: 0.294 AC XY: 206868 AN XY: 704202

Gnomad4 AFR exome AF: 0.248

Gnomad4 AMR exome AF: 0.191

Gnomad4 ASJ exome AF: 0.339

Gnomad4 EAS exome AF: 0.229

Gnomad4 SAS exome AF: 0.254

Gnomad4 FIN exome AF: 0.292

Gnomad4 NFE exome AF: 0.302

Gnomad4 OTH exome AF: 0.296

GnomAD4 genome AF: 0.282 AC: 42911 AN: 152110 Hom.: 6183 Cov.: 32 AF XY: 0.281 AC XY: 20926 AN XY: 74354

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.309

Alfa AF: 0.305 Hom.: 12740

Bravo AF: 0.281

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.3
Dann	Benign	0.88

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: rs571199; hg19: chr1-55139618; COSMIC: COSV59869698; COSMIC: COSV59869698;