Variant 6-151405694-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_017909.4(RMND1):c.1317+26G>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 1,091,798 control chromosomes in the GnomAD database, including 55,637 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.37 ( 12953 hom., cov: 32)

Exomes 𝑓: 0.28 ( 42684 hom. )

Consequence

RMND1
NM_017909.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.535

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=-0.89).

BP6

Variant 6-151405694-C-T is Benign according to our data. Variant chr6-151405694-C-T is described in ClinVar as [Benign]. Clinvar id is 1223720.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
RMND1	NM_017909.4 linkuse as main transcript	c.1317+26G>A	intron_variant	ENST00000444024.3
RMND1	NM_001271937.2 linkuse as main transcript	c.807+26G>A	intron_variant
RMND1	XM_047418959.1 linkuse as main transcript	c.1317+26G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMND1	ENST00000444024.3 linkuse as main transcript	c.1317+26G>A		intron_variant		3	NM_017909.4	P1	Q9NWS8-1

Frequencies

GnomAD3 genomes

AF:

0.374

AC:

56823

AN:

151876

Hom.:

12923

Cov.:

show subpopulations

Gnomad AFR

AF:

0.614

Gnomad AMI

AF:

0.297

Gnomad AMR

AF:

0.353

Gnomad ASJ

AF:

0.300

Gnomad EAS

AF:

0.692

Gnomad SAS

AF:

0.382

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.233

Gnomad OTH

AF:

0.355

GnomAD3 exomes

AF:

0.332

AC:

81431

AN:

244956

Hom.:

16338

AF XY:

0.325

AC XY:

43048

AN XY:

132468

show subpopulations

Gnomad AFR exome

AF:

0.620

Gnomad AMR exome

AF:

0.354

Gnomad ASJ exome

AF:

0.293

Gnomad EAS exome

AF:

0.707

Gnomad SAS exome

AF:

0.373

Gnomad FIN exome

AF:

0.253

Gnomad NFE exome

AF:

0.233

Gnomad OTH exome

AF:

0.294

GnomAD4 exome

AF:

0.279

AC:

262434

AN:

939804

Hom.:

42684

Cov.:

AF XY:

0.280

AC XY:

137103

AN XY:

489266

show subpopulations

Gnomad4 AFR exome

AF:

0.623

Gnomad4 AMR exome

AF:

0.359

Gnomad4 ASJ exome

AF:

0.296

Gnomad4 EAS exome

AF:

0.615

Gnomad4 SAS exome

AF:

0.375

Gnomad4 FIN exome

AF:

0.251

Gnomad4 NFE exome

AF:

0.230

Gnomad4 OTH exome

AF:

0.310

GnomAD4 genome

AF:

0.374

AC:

56908

AN:

151994

Hom.:

12953

Cov.:

AF XY:

0.378

AC XY:

28058

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.614

Gnomad4 AMR

AF:

0.353

Gnomad4 ASJ

AF:

0.300

Gnomad4 EAS

AF:

0.691

Gnomad4 SAS

AF:

0.381

Gnomad4 FIN

AF:

0.253

Gnomad4 NFE

AF:

0.233

Gnomad4 OTH

AF:

0.363

Alfa

AF:

0.249

Hom.:

6037

Bravo

AF:

0.395

Asia WGS

AF:

0.551

AC:

1912

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.12

DANN

Benign

0.41

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