6-151404858-C-CATTT

Variant names:

• chr6-151404858-C-CATTT
• rs35871051
• NM_017909.4:c.*373_*376dupAAAT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_017909.4(RMND1):​c.*373_*376dupAAAT 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
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• combined oxidative phosphorylation defect type 11

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017909.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMND1	NM_017909.4	MANE Select	c.*373_*376dupAAAT		3_prime_UTR	Exon 12 of 12	NP_060379.2	Q9NWS8-1
	RMND1	NM_001271937.2		c.*373_*376dupAAAT		3_prime_UTR	Exon 11 of 11	NP_001258866.1	A0A087WXU0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMND1	ENST00000444024.3	TSL:3 MANE Select	c.*373_*376dupAAAT		3_prime_UTR	Exon 12 of 12	ENSP00000412708.2	Q9NWS8-1
	RMND1	ENST00000938884.1		c.*373_*376dupAAAT		splice_region	Exon 12 of 12	ENSP00000608943.1
	RMND1	ENST00000683724.1		c.*373_*376dupAAAT		3_prime_UTR	Exon 12 of 12	ENSP00000507984.1	Q9NWS8-1

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

African (AFR) AF: 0.423 AC: 71 AN: 168

American (AMR) AF: 0.261 AC: 111 AN: 426

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 40 AN: 282

East Asian (EAS) AF: 0.454 AC: 109 AN: 240

South Asian (SAS) AF: 0.253 AC: 220 AN: 868

European-Finnish (FIN) AF: 0.159 AC: 66 AN: 414

Middle Eastern (MID) AF: 0.190 AC: 11 AN: 58

European-Non Finnish (NFE) AF: 0.132 AC: 1130 AN: 8546

Other (OTH) AF: 0.189 AC: 147 AN: 778

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

African (AFR) AF: 0.598 AC: 24549 AN: 41066

American (AMR) AF: 0.351 AC: 5334 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1042 AN: 3470

East Asian (EAS) AF: 0.677 AC: 3453 AN: 5102

South Asian (SAS) AF: 0.379 AC: 1818 AN: 4794

European-Finnish (FIN) AF: 0.248 AC: 2601 AN: 10472

Middle Eastern (MID) AF: 0.293 AC: 85 AN: 290

European-Non Finnish (NFE) AF: 0.232 AC: 15726 AN: 67874

Other (OTH) AF: 0.356 AC: 747 AN: 2100

Alfa AF: 0.0791 Hom.: 103

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs35871051; hg19: chr6-151725993;