rs6588528

chr1-54691208-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.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

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=-0.93).
• 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/exons	MANE	UniProt
MROH7	NM_001039464.4	c.2712-1216G>A		intron_variant		ENST00000421030.7
MROH7-TTC4	NR_037639.2	n.3246-1216G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MROH7	ENST00000421030.7	c.2712-1216G>A		intron_variant		2	NM_001039464.4	P2

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

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.233

Alfa AF: 0.179 Hom.: 5271

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

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: rs6588528; hg19: chr1-55156881;