Genetic Variant RMND1:c.*195C>A (chr6-151405040-G-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_017909.4(RMND1):c.*195C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 499,788 control chromosomes in the GnomAD database, including 28,779 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.37 ( 12556 hom., cov: 31)

Exomes 𝑓: 0.28 ( 16223 hom. )

Consequence

RMND1
NM_017909.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.385

Variant links:

Genes affected

RMND1 (HGNC:21176): (required for meiotic nuclear division 1 homolog) The protein encoded by this gene belongs to the evolutionary conserved sif2 family of proteins that share the DUF155 domain in common. This protein is thought to be localized in the mitochondria and involved in mitochondrial translation. Mutations in this gene are associated with combined oxidative phosphorylation deficiency-11. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2012]

RMND1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 6-151405040-G-T is Benign according to our data. Variant chr6-151405040-G-T is described in ClinVar as [Benign]. Clinvar id is 1241989.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
RMND1	NM_017909.4 link	c.*195C>A	3_prime_UTR_variant	Exon 12 of 12	ENST00000444024.3	NP_060379.2	Q9NWS8-1
RMND1	NM_001271937.2 link	c.*195C>A	3_prime_UTR_variant	Exon 11 of 11		NP_001258866.1	Q9NWS8A0A087WXU0
RMND1	XM_047418959.1 link	c.*195C>A	3_prime_UTR_variant	Exon 12 of 13		XP_047274915.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMND1	ENST00000444024 link	c.*195C>A		3_prime_UTR_variant	Exon 12 of 12	3	NM_017909.4	ENSP00000412708.2		Q9NWS8-1

Frequencies

GnomAD3 genomes

AF:

0.370

AC:

56133

AN:

151662

Hom.:

12530

Cov.:

show subpopulations

Gnomad AFR

AF:

0.602

Gnomad AMI

AF:

0.298

Gnomad AMR

AF:

0.352

Gnomad ASJ

AF:

0.300

Gnomad EAS

AF:

0.683

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.350

GnomAD4 exome

AF:

0.280

AC:

97325

AN:

348008

Hom.:

16223

Cov.:

AF XY:

0.283

AC XY:

52317

AN XY:

184812

show subpopulations

Gnomad4 AFR exome

AF:

0.589

Gnomad4 AMR exome

AF:

0.353

Gnomad4 ASJ exome

AF:

0.287

Gnomad4 EAS exome

AF:

0.575

Gnomad4 SAS exome

AF:

0.371

Gnomad4 FIN exome

AF:

0.240

Gnomad4 NFE exome

AF:

0.223

Gnomad4 OTH exome

AF:

0.298

GnomAD4 genome

AF:

0.370

AC:

56212

AN:

151780

Hom.:

12556

Cov.:

AF XY:

0.373

AC XY:

27696

AN XY:

74166

show subpopulations

Gnomad4 AFR

AF:

0.602

Gnomad4 AMR

AF:

0.352

Gnomad4 ASJ

AF:

0.300

Gnomad4 EAS

AF:

0.682

Gnomad4 SAS

AF:

0.380

Gnomad4 FIN

AF:

0.253

Gnomad4 NFE

AF:

0.232

Gnomad4 OTH

AF:

0.357

Alfa

AF:

0.303

Hom.:

1091

Bravo

AF:

0.390

Asia WGS

AF:

0.533

AC:

1850

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 23, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.52

DANN

Benign

0.68

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over