rs7204628

Variant names:

• chr16-11350715-A-C
• rs7204628
• NM_152308.3:c.369A>C

Your query was ambiguous. Multiple possible variants found:

• chr16-11350715-A-C
• chr16-11350715-A-G
• chr16-11350715-A-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_152308.3(RMI2):​c.369A>C​(p.Thr123Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 1,612,614 control chromosomes in the GnomAD database, including 48,024 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.22 (4006 hom., cov: 33)
  • Exomes 𝑓: 0.24 (44018 hom.)
• Consequence: RMI2 NM_152308.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 19 publications found

Genes affected

RMI2 (HGNC:28349): (RecQ mediated genome instability 2) RMI2 is a component of the BLM (RECQL3; MIM 604610) complex, which plays a role in homologous recombination-dependent DNA repair and is essential for genome stability (Xu et al., 2008 [PubMed 18923082]).[supplied by OMIM, Nov 2008]

LOC105371082 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BP7: Synonymous conserved (PhyloP=-0.458 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152308.3. 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
	RMI2	NM_152308.3	MANE Select	c.369A>C	p.Thr123Thr	synonymous	Exon 2 of 2	NP_689521.1	Q96E14-1
	RMI2	NR_130754.2		n.159A>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMI2	ENST00000312499.6	TSL:1 MANE Select	c.369A>C	p.Thr123Thr	synonymous	Exon 2 of 2	ENSP00000310356.5	Q96E14-1
	RMI2	ENST00000572173.1	TSL:1	c.180A>C	p.Thr60Thr	synonymous	Exon 5 of 5	ENSP00000461206.1	Q96E14-2
	RMI2	ENST00000576027.1	TSL:2	c.*62A>C		3_prime_UTR	Exon 2 of 2	ENSP00000459601.1	I3L2E0

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34111 AN: 152050 Hom.: 4003 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.00827

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.228

GnomAD2 exomes AF: 0.196 AC: 49136 AN: 250918 AF XY: 0.199

Gnomad AFR exome AF: 0.237

Gnomad AMR exome AF: 0.127

Gnomad ASJ exome AF: 0.180

Gnomad EAS exome AF: 0.00489

Gnomad FIN exome AF: 0.236

Gnomad NFE exome AF: 0.238

Gnomad OTH exome AF: 0.212

GnomAD4 exome AF: 0.239 AC: 348459 AN: 1460446 Hom.: 44018 Cov.: 32 AF XY: 0.236 AC XY: 171155 AN XY: 726566

African (AFR) AF: 0.234 AC: 7819 AN: 33422

American (AMR) AF: 0.135 AC: 6052 AN: 44668

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 4722 AN: 26102

East Asian (EAS) AF: 0.00375 AC: 149 AN: 39692

South Asian (SAS) AF: 0.178 AC: 15336 AN: 86144

European-Finnish (FIN) AF: 0.240 AC: 12795 AN: 53396

Middle Eastern (MID) AF: 0.186 AC: 1070 AN: 5766

European-Non Finnish (NFE) AF: 0.258 AC: 286741 AN: 1110924

Other (OTH) AF: 0.228 AC: 13775 AN: 60332

GnomAD4 genome AF: 0.224 AC: 34114 AN: 152168 Hom.: 4006 Cov.: 33 AF XY: 0.221 AC XY: 16437 AN XY: 74388

African (AFR) AF: 0.239 AC: 9930 AN: 41492

American (AMR) AF: 0.185 AC: 2832 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3472

East Asian (EAS) AF: 0.00829 AC: 43 AN: 5188

South Asian (SAS) AF: 0.175 AC: 844 AN: 4824

European-Finnish (FIN) AF: 0.231 AC: 2441 AN: 10582

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16600 AN: 67992

Other (OTH) AF: 0.227 AC: 479 AN: 2114

Alfa AF: 0.212 Hom.: 2624

Bravo AF: 0.219

Asia WGS AF: 0.126 AC: 442 AN: 3478

EpiCase AF: 0.240

EpiControl AF: 0.226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	2.4
DANN	Benign	0.82
PhyloP100		-0.46
Mutation Taster		=98/2	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7204628; hg19: chr16-11444572; COSMIC: COSV56963902; COSMIC: COSV56963902;