dbSNP rs2233837: REM1:c.*167G>A (chr20-31484597-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014012.6(REM1):c.*167G>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 0.00428 in 882,908 control chromosomes in the GnomAD database, including 85 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 0.017 ( 62 hom., cov: 33)

Exomes 𝑓: 0.0016 ( 23 hom. )

Consequence

REM1
NM_014012.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.407

Publications

1 publications found

Variant links:

Genes affected

REM1 (HGNC:15922): (RRAD and GEM like GTPase 1) The protein encoded by this gene is a GTPase and member of the RAS-like GTP-binding protein family. The encoded protein is expressed in endothelial cells, where it promotes reorganization of the actin cytoskeleton and morphological changes in the cells. [provided by RefSeq, Jul 2008]

REM1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
REM1	NM_014012.6 link	c.*167G>A	3_prime_UTR_variant	Exon 5 of 5	ENST00000201979.3	NP_054731.2	O75628
REM1	XM_005260404.1 link	c.*167G>A	3_prime_UTR_variant	Exon 5 of 5		XP_005260461.1
REM1	XM_017027833.2 link	c.*167G>A	3_prime_UTR_variant	Exon 5 of 5		XP_016883322.1
REM1	XM_011528795.1 link	c.*167G>A	3_prime_UTR_variant	Exon 5 of 5		XP_011527097.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
REM1	ENST00000201979.3 link	c.*167G>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_014012.6	ENSP00000201979.2		O75628

Frequencies

GnomAD3 genomes

AF:

0.0169

AC:

2580

AN:

152240

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0584

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00693

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000235

Gnomad OTH

AF:

0.0148

GnomAD4 exome

AF:

0.00162

AC:

1187

AN:

730550

Hom.:

Cov.:

AF XY:

0.00142

AC XY:

517

AN XY:

363648

show subpopulations

African (AFR)

AF:

0.0615

AC:

887

AN:

14416

American (AMR)

AF:

0.00522

AC:

AN:

10736

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14062

East Asian (EAS)

AF:

0.00

AC:

AN:

26120

South Asian (SAS)

AF:

0.000225

AC:

AN:

39914

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30066

Middle Eastern (MID)

AF:

0.00483

AC:

AN:

2486

European-Non Finnish (NFE)

AF:

0.000107

AC:

AN:

558366

Other (OTH)

AF:

0.00474

AC:

163

AN:

34384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

120

179

239

299

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0170

AC:

2589

AN:

152358

Hom.:

Cov.:

AF XY:

0.0165

AC XY:

1227

AN XY:

74514

show subpopulations

African (AFR)

AF:

0.0584

AC:

2429

AN:

41590

American (AMR)

AF:

0.00692

AC:

106

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5186

South Asian (SAS)

AF:

0.00103

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000235

AC:

AN:

68022

Other (OTH)

AF:

0.0147

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

134

267

401

534

668

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00853

Hom.:

Bravo

AF:

0.0198

Asia WGS

AF:

0.00375

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.74

(source)

DANN

Benign

0.47

PhyloP100

-0.41

Mutation Taster

=99/1

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over