chr1-54653520-A-G

Position:

• chr1-54653520-A-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001039464.4(MROH7):​c.594A>G​(p.Ser198=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,614,156 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0020 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0022 (9 hom.)
• Consequence: MROH7 NM_001039464.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.208

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 -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 1-54653520-A-G is Benign according to our data. Variant chr1-54653520-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2638831.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.208 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MROH7	NM_001039464.4	c.594A>G	p.Ser198=	synonymous_variant	3/24	ENST00000421030.7
MROH7-TTC4	NR_037639.2	n.1037A>G		non_coding_transcript_exon_variant	3/33

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MROH7	ENST00000421030.7	c.594A>G	p.Ser198=	synonymous_variant	3/24	2	NM_001039464.4	P2

Frequencies

GnomAD3 genomes AF: 0.00196 AC: 298 AN: 152168 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000603

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00373

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00321

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00238

Gnomad OTH AF: 0.00430

GnomAD3 exomes AF: 0.00223 AC: 557 AN: 249250 Hom.: 1 AF XY: 0.00225 AC XY: 304 AN XY: 135224

Gnomad AFR exome AF: 0.000323

Gnomad AMR exome AF: 0.00249

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00216

Gnomad FIN exome AF: 0.00441

Gnomad NFE exome AF: 0.00257

Gnomad OTH exome AF: 0.00231

GnomAD4 exome AF: 0.00224 AC: 3275 AN: 1461870 Hom.: 9 Cov.: 64 AF XY: 0.00237 AC XY: 1727 AN XY: 727238

Gnomad4 AFR exome AF: 0.000269

Gnomad4 AMR exome AF: 0.00253

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00274

Gnomad4 FIN exome AF: 0.00384

Gnomad4 NFE exome AF: 0.00236

Gnomad4 OTH exome AF: 0.00147

GnomAD4 genome AF: 0.00196 AC: 298 AN: 152286 Hom.: 0 Cov.: 32 AF XY: 0.00185 AC XY: 138 AN XY: 74464

Gnomad4 AFR AF: 0.000601

Gnomad4 AMR AF: 0.00373

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.00321

Gnomad4 NFE AF: 0.00238

Gnomad4 OTH AF: 0.00426

Alfa AF: 0.00194 Hom.: 0

Bravo AF: 0.00202

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.00218

EpiControl AF: 0.00267

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2022

MROH7: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.54

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: rs41297847; hg19: chr1-55119193;