dbSNP rs1051760: REPIN1:c.*596A>G (chr7-150373541-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001099695.2(REPIN1):c.*596A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 169,878 control chromosomes in the GnomAD database, including 14,127 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 0.39 ( 12607 hom., cov: 33)

Exomes 𝑓: 0.41 ( 1520 hom. )

Consequence

REPIN1
NM_001099695.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.300

Publications

19 publications found

Variant links:

Genes affected

REPIN1 (HGNC:17922): (replication initiator 1) Enables RNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of glucose import and regulation of fatty acid transport. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

REPIN1 links:

ZNF775 (HGNC:28501): (zinc finger protein 775) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF775 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
REPIN1	NM_001099695.2 link	c.*596A>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000489432.7	NP_001093165.1	Q9BWE0-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
REPIN1	ENST00000489432.7 link	c.*596A>G		3_prime_UTR_variant	Exon 3 of 3	2	NM_001099695.2	ENSP00000417291.2		Q9BWE0-4

Frequencies

GnomAD3 genomes

AF:

0.394

AC:

59906

AN:

151878

Hom.:

12583

Cov.:

show subpopulations

Gnomad AFR

AF:

0.527

Gnomad AMI

AF:

0.409

Gnomad AMR

AF:

0.260

Gnomad ASJ

AF:

0.429

Gnomad EAS

AF:

0.497

Gnomad SAS

AF:

0.479

Gnomad FIN

AF:

0.434

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.323

Gnomad OTH

AF:

0.342

GnomAD4 exome

AF:

0.406

AC:

7264

AN:

17882

Hom.:

1520

Cov.:

AF XY:

0.408

AC XY:

3518

AN XY:

8624

show subpopulations

African (AFR)

AF:

0.563

AC:

AN:

American (AMR)

AF:

0.233

AC:

178

AN:

764

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.496

AC:

139

AN:

280

European-Finnish (FIN)

AF:

0.428

AC:

6187

AN:

14472

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.313

AC:

662

AN:

2114

Other (OTH)

AF:

0.377

AC:

AN:

212

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

165

330

494

659

824

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.395

AC:

59972

AN:

151996

Hom.:

12607

Cov.:

AF XY:

0.403

AC XY:

29901

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.528

AC:

21888

AN:

41454

American (AMR)

AF:

0.259

AC:

3961

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.429

AC:

1488

AN:

3468

East Asian (EAS)

AF:

0.497

AC:

2565

AN:

5158

South Asian (SAS)

AF:

0.478

AC:

2308

AN:

4824

European-Finnish (FIN)

AF:

0.434

AC:

4579

AN:

10548

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.323

AC:

21972

AN:

67944

Other (OTH)

AF:

0.341

AC:

721

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1802

3604

5405

7207

9009

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.347

Hom.:

31073

Bravo

AF:

0.385

Asia WGS

AF:

0.475

AC:

1653

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

8.5

(source)

DANN

Benign

0.43

PhyloP100

0.30

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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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rs1051760

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