rs1982151

Variant names:

• chr9-84002350-A-C
• rs1982151
• NM_001358291.2:c.1364A>C

Your query was ambiguous. Multiple possible variants found:

• chr9-84002350-A-C
• chr9-84002350-A-G
• chr9-84002350-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001358291.2(RMI1):​c.1364A>C​(p.Asn455Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N455S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RMI1 NM_001358291.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353

Genes affected

RMI1 (HGNC:25764): (RecQ mediated genome instability 1) Predicted to enable nucleotide binding activity. Predicted to be involved in double-strand break repair via homologous recombination and resolution of meiotic recombination intermediates. Predicted to act upstream of or within glucose homeostasis; reduction of food intake in response to dietary excess; and response to glucose. Located in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.03529355).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RMI1	NM_001358291.2	c.1364A>C	p.Asn455Thr	missense_variant	Exon 3 of 3	ENST00000445877.6	NP_001345220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMI1	ENST00000445877.6	c.1364A>C	p.Asn455Thr	missense_variant	Exon 3 of 3	1	NM_001358291.2	ENSP00000402433.2
RMI1	ENST00000325875.7	c.1364A>C	p.Asn455Thr	missense_variant	Exon 3 of 3	2		ENSP00000317039.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.073
BayesDel_addAF	Benign	-0.51	T
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.1
DANN	Benign	0.15
DEOGEN2	Benign	0.036	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.068	N
LIST_S2	Benign	0.24	T
M_CAP	Benign	0.0036	T
MetaRNN	Benign	0.035	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	N
PrimateAI	Benign	0.27	T
PROVEAN	Benign	0.47	N
REVEL	Benign	0.011
Sift	Benign	0.12	T
Sift4G	Benign	0.62	T
Polyphen		0.0	B
Vest4		0.054
MutPred		0.11		Loss of methylation at K453 (P = 0.0944);
MVP		0.13
MPC		0.074
ClinPred		0.040	T
GERP RS		-3.0
Varity_R		0.035
gMVP		0.16

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: rs1982151; hg19: chr9-86617265;