dbSNP rs571199: MROH7:c.1801-71G>A (chr1-54673945-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.547

Publications

9 publications found

Variant links:

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 links:

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]

MROH7-TTC4 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MROH7	NM_001039464.4 link	c.1801-71G>A		intron_variant	Intron 9 of 23	ENST00000421030.7	NP_001034553.3	Q68CQ1-7B7Z7S6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MROH7	ENST00000421030.7 link	c.1801-71G>A		intron_variant	Intron 9 of 23	2	NM_001039464.4	ENSP00000396622.2		Q68CQ1-7
MROH7-TTC4	ENST00000414150.6 link	n.1801-71G>A		intron_variant	Intron 9 of 32	2		ENSP00000410192.2		A0A0A0MT08

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42906

AN:

151992

Hom.:

6188

Cov.:

show subpopulations

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.:

AF XY:

0.294

AC XY:

206868

AN XY:

704202

show subpopulations

African (AFR)

AF:

0.248

AC:

8093

AN:

32588

American (AMR)

AF:

0.191

AC:

8315

AN:

43554

Ashkenazi Jewish (ASJ)

AF:

0.339

AC:

8264

AN:

24402

East Asian (EAS)

AF:

0.229

AC:

9043

AN:

39428

South Asian (SAS)

AF:

0.254

AC:

20971

AN:

82574

European-Finnish (FIN)

AF:

0.292

AC:

15330

AN:

52414

Middle Eastern (MID)

AF:

0.413

AC:

2273

AN:

5506

European-Non Finnish (NFE)

AF:

0.302

AC:

324929

AN:

1076714

Other (OTH)

AF:

0.296

AC:

17380

AN:

58710

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

14451

28902

43352

57803

72254

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10478

20956

31434

41912

52390

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.282

AC:

42911

AN:

152110

Hom.:

6183

Cov.:

AF XY:

0.281

AC XY:

20926

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.247

AC:

10263

AN:

41518

American (AMR)

AF:

0.258

AC:

3939

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.341

AC:

1183

AN:

3470

East Asian (EAS)

AF:

0.233

AC:

1207

AN:

5174

South Asian (SAS)

AF:

0.239

AC:

1148

AN:

4810

European-Finnish (FIN)

AF:

0.294

AC:

3100

AN:

10558

Middle Eastern (MID)

AF:

0.401

AC:

118

AN:

294

European-Non Finnish (NFE)

AF:

0.307

AC:

20898

AN:

67986

Other (OTH)

AF:

0.309

AC:

651

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1554

3109

4663

6218

7772

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

436

872

1308

1744

2180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.299

Hom.:

19693

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

(source)

DANN

Benign

0.88

PhyloP100

-0.55

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over