chr6-151405040-G-T

Position:

• chr6-151405040-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.385

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 -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	HGVSp	Effect	#exon/exons	MANE	UniProt
RMND1	NM_017909.4	c.*195C>A		3_prime_UTR_variant	12/12	ENST00000444024.3
RMND1	NM_001271937.2	c.*195C>A		3_prime_UTR_variant	11/11
RMND1	XM_047418959.1	c.*195C>A		3_prime_UTR_variant	12/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMND1	ENST00000444024.3	c.*195C>A		3_prime_UTR_variant	12/12	3	NM_017909.4	P1

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56133 AN: 151662 Hom.: 12530 Cov.: 31

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.: 3 AF XY: 0.283 AC XY: 52317 AN XY: 184812

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.: 31 AF XY: 0.373 AC XY: 27696 AN XY: 74166

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

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	-0.93
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

Other links and lift over

dbSNP: rs3757312; hg19: chr6-151726175;