dbSNP rs1051764: REPIN1:c.*629T>C (chr7-150373574-T-C) – 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.*629T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 168,834 control chromosomes in the GnomAD database, including 12,711 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 0.38 ( 11245 hom., cov: 33)

Exomes 𝑓: 0.41 ( 1466 hom. )

Consequence

REPIN1
NM_001099695.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.560

Publications

18 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:

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
REPIN1	NM_001099695.2 link	c.*629T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000489432.7	NP_001093165.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
REPIN1	ENST00000489432.7 link	c.*629T>C		3_prime_UTR_variant	Exon 3 of 3	2	NM_001099695.2	ENSP00000417291.2

Frequencies

GnomAD3 genomes

AF:

0.376

AC:

57122

AN:

151942

Hom.:

11234

Cov.:

show subpopulations

Gnomad AFR

AF:

0.462

Gnomad AMI

AF:

0.407

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.429

Gnomad EAS

AF:

0.497

Gnomad SAS

AF:

0.479

Gnomad FIN

AF:

0.433

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.323

Gnomad OTH

AF:

0.333

GnomAD4 exome

AF:

0.412

AC:

6911

AN:

16774

Hom.:

1466

Cov.:

AF XY:

0.413

AC XY:

3329

AN XY:

8054

show subpopulations

African (AFR)

AF:

0.400

AC:

AN:

American (AMR)

AF:

0.220

AC:

AN:

400

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.333

AC:

AN:

South Asian (SAS)

AF:

0.485

AC:

AN:

136

European-Finnish (FIN)

AF:

0.428

AC:

6209

AN:

14502

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.310

AC:

475

AN:

1534

Other (OTH)

AF:

0.355

AC:

AN:

172

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

155

310

464

619

774

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.376

AC:

57171

AN:

152060

Hom.:

11245

Cov.:

AF XY:

0.385

AC XY:

28593

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.463

AC:

19194

AN:

41468

American (AMR)

AF:

0.254

AC:

3877

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.429

AC:

1489

AN:

3470

East Asian (EAS)

AF:

0.498

AC:

2571

AN:

5166

South Asian (SAS)

AF:

0.478

AC:

2305

AN:

4822

European-Finnish (FIN)

AF:

0.433

AC:

4581

AN:

10572

Middle Eastern (MID)

AF:

0.391

AC:

115

AN:

294

European-Non Finnish (NFE)

AF:

0.323

AC:

21968

AN:

67960

Other (OTH)

AF:

0.333

AC:

701

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1807

3615

5422

7230

9037

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

562

1124

1686

2248

2810

<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:

0.354

Hom.:

11277

Bravo

AF:

0.364

Asia WGS

AF:

0.472

AC:

1642

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.0

(source)

DANN

Benign

0.49

PhyloP100

-0.56

Mutation Taster

=100/0

polymorphism (auto)

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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