chr6-151405621-T-C

Position:

• chr6-151405621-T-C

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.1317+99A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 680,652 control chromosomes in the GnomAD database, including 38,347 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.37 (12429 hom., cov: 32)
  • Exomes 𝑓: 0.29 (25918 hom.)
• Consequence: RMND1 NM_017909.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.825

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=-0.9).
• BP6: Variant 6-151405621-T-C is Benign according to our data. Variant chr6-151405621-T-C is described in ClinVar as [Benign]. Clinvar id is 1291373.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RMND1	NM_017909.4	c.1317+99A>G		intron_variant		ENST00000444024.3
RMND1	NM_001271937.2	c.807+99A>G		intron_variant
RMND1	XM_047418959.1	c.1317+99A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMND1	ENST00000444024.3	c.1317+99A>G		intron_variant		3	NM_017909.4	P1

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55992 AN: 151990 Hom.: 12403 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.349

GnomAD4 exome AF: 0.290 AC: 153019 AN: 528544 Hom.: 25918 AF XY: 0.290 AC XY: 81591 AN XY: 281556

Gnomad4 AFR exome AF: 0.599

Gnomad4 AMR exome AF: 0.358

Gnomad4 ASJ exome AF: 0.299

Gnomad4 EAS exome AF: 0.600

Gnomad4 SAS exome AF: 0.371

Gnomad4 FIN exome AF: 0.247

Gnomad4 NFE exome AF: 0.230

Gnomad4 OTH exome AF: 0.304

GnomAD4 genome AF: 0.369 AC: 56070 AN: 152108 Hom.: 12429 Cov.: 32 AF XY: 0.371 AC XY: 27625 AN XY: 74362

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.356

Alfa AF: 0.311 Hom.: 1355

Bravo AF: 0.389

Asia WGS AF: 0.532 AC: 1847 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	-0.90
CADD	Benign	0.28
DANN	Benign	0.80

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: rs3757314; hg19: chr6-151726756; COSMIC: COSV60549963; COSMIC: COSV60549963;