chr6-151404858-C-CATTT

Position:

• chr6-151404858-C-CATTT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_017909.4(RMND1):​c.*376_*377insAAAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.37 (12298 hom., cov: 0)
  • Exomes 𝑓: 0.16 (231 hom.)
• Consequence: RMND1 NM_017909.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.479

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-151404858-C-CATTT is Benign according to our data. Variant chr6-151404858-C-CATTT is described in ClinVar as [Benign]. Clinvar id is 1267543.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RMND1	NM_017909.4	c.*376_*377insAAAT		3_prime_UTR_variant	12/12	ENST00000444024.3
RMND1	NM_001271937.2	c.*376_*377insAAAT		3_prime_UTR_variant	11/11
RMND1	XM_047418959.1	c.*208-61_*208-60insAAAT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMND1	ENST00000444024.3	c.*376_*377insAAAT		3_prime_UTR_variant	12/12	3	NM_017909.4	P1

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55548 AN: 151150 Hom.: 12273 Cov.: 0

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.348

GnomAD4 exome AF: 0.162 AC: 1905 AN: 11780 Hom.: 231 Cov.: 0 AF XY: 0.163 AC XY: 961 AN XY: 5888

Gnomad4 AFR exome AF: 0.423

Gnomad4 AMR exome AF: 0.261

Gnomad4 ASJ exome AF: 0.142

Gnomad4 EAS exome AF: 0.454

Gnomad4 SAS exome AF: 0.253

Gnomad4 FIN exome AF: 0.159

Gnomad4 NFE exome AF: 0.132

Gnomad4 OTH exome AF: 0.189

GnomAD4 genome AF: 0.368 AC: 55625 AN: 151268 Hom.: 12298 Cov.: 0 AF XY: 0.370 AC XY: 27382 AN XY: 73906

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.356

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 27, 2020

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs35871051; hg19: chr6-151725993;