dbSNP rs28369942: REV1:c.-10-115_-10-114insGACTT (chr2-99465099-A-AAAGTC) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_016316.4(REV1):c.-10-115_-10-114insGACTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 852,336 control chromosomes in the GnomAD database, including 138,195 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.61 ( 29248 hom., cov: 0)

Exomes 𝑓: 0.54 ( 108947 hom. )

Consequence

REV1
NM_016316.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.32

Publications

7 publications found

Variant links:

Genes affected

REV1 (HGNC:14060): (REV1 DNA directed polymerase) This gene encodes a protein with similarity to the S. cerevisiae mutagenesis protein Rev1. The Rev1 proteins contain a BRCT domain, which is important in protein-protein interactions. A suggested role for the human Rev1-like protein is as a scaffold that recruits DNA polymerases involved in translesion synthesis (TLS) of damaged DNA. [provided by RefSeq, Mar 2016]

REV1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016316.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
REV1	NM_016316.4	MANE Select	c.-10-115_-10-114insGACTT	intron	N/A	NP_057400.1
REV1	NM_001321454.2		c.-10-115_-10-114insGACTT	intron	N/A	NP_001308383.1
REV1	NM_001037872.3		c.-10-115_-10-114insGACTT	intron	N/A	NP_001032961.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
REV1	ENST00000258428.8	TSL:1 MANE Select	c.-10-115_-10-114insGACTT	intron	N/A	ENSP00000258428.3
REV1	ENST00000393445.7	TSL:1	c.-10-115_-10-114insGACTT	intron	N/A	ENSP00000377091.3
REV1	ENST00000413697.5	TSL:2	n.-10-115_-10-114insGACTT	intron	N/A	ENSP00000416274.1

Frequencies

GnomAD3 genomes

AF:

0.613

AC:

92830

AN:

151516

Hom.:

29193

Cov.:

show subpopulations

Gnomad AFR

AF:

0.736

Gnomad AMI

AF:

0.585

Gnomad AMR

AF:

0.658

Gnomad ASJ

AF:

0.499

Gnomad EAS

AF:

0.361

Gnomad SAS

AF:

0.516

Gnomad FIN

AF:

0.668

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.553

Gnomad OTH

AF:

0.574

GnomAD4 exome

AF:

0.544

AC:

381466

AN:

700706

Hom.:

108947

AF XY:

0.540

AC XY:

197994

AN XY:

366518

show subpopulations

African (AFR)

AF:

0.736

AC:

12163

AN:

16522

American (AMR)

AF:

0.701

AC:

18081

AN:

25780

Ashkenazi Jewish (ASJ)

AF:

0.474

AC:

8551

AN:

18052

East Asian (EAS)

AF:

0.340

AC:

10905

AN:

32100

South Asian (SAS)

AF:

0.497

AC:

27895

AN:

56156

European-Finnish (FIN)

AF:

0.645

AC:

30148

AN:

46720

Middle Eastern (MID)

AF:

0.465

AC:

1825

AN:

3926

European-Non Finnish (NFE)

AF:

0.542

AC:

253455

AN:

467616

Other (OTH)

AF:

0.545

AC:

18443

AN:

33834

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

8021

16042

24064

32085

40106

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4206

8412

12618

16824

21030

<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:

0.613

AC:

92939

AN:

151630

Hom.:

29248

Cov.:

AF XY:

0.615

AC XY:

45601

AN XY:

74088

show subpopulations

African (AFR)

AF:

0.737

AC:

30425

AN:

41310

American (AMR)

AF:

0.658

AC:

10042

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.499

AC:

1729

AN:

3464

East Asian (EAS)

AF:

0.360

AC:

1866

AN:

5178

South Asian (SAS)

AF:

0.515

AC:

2477

AN:

4808

European-Finnish (FIN)

AF:

0.668

AC:

7013

AN:

10494

Middle Eastern (MID)

AF:

0.486

AC:

142

AN:

292

European-Non Finnish (NFE)

AF:

0.553

AC:

37520

AN:

67828

Other (OTH)

AF:

0.571

AC:

1202

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1763

3526

5289

7052

8815

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

748

1496

2244

2992

3740

<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:

0.593

Hom.:

2869

Bravo

AF:

0.620

Asia WGS

AF:

0.481

AC:

1668

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over