rs864687

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_021930.6(RINT1):c.2067+13A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0678 in 1,612,222 control chromosomes in the GnomAD database, including 4,761 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1208 hom., cov: 33)

Exomes 𝑓: 0.064 ( 3553 hom. )

Consequence

RINT1
NM_021930.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.279

Publications

9 publications found

Variant links:

Genes affected

RINT1 (HGNC:21876): (RAD50 interactor 1) This gene encodes a protein first identified for its ability to interact with the RAD50 double strand break repair protein, with the resulting interaction implicated in the regulation of cell cycle progression and telomere length. The encoded protein may also play a role in trafficking of cellular cargo from the endosome to the trans-Golgi network. Mutations in this gene may be associated with breast cancer in human patients. [provided by RefSeq, Oct 2016]

RINT1 links:

EFCAB10 (HGNC:34531): (EF-hand calcium binding domain 10) Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

EFCAB10 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 7-105565470-A-C is Benign according to our data. Variant chr7-105565470-A-C is described in ClinVar as [Benign]. Clinvar id is 403379.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RINT1	NM_021930.6 link	c.2067+13A>C		intron_variant	Intron 13 of 14	ENST00000257700.7	NP_068749.3	Q6NUQ1
EFCAB10	NM_001355526.2 link	c.384-23T>G		intron_variant	Intron 4 of 4	ENST00000480514.6	NP_001342455.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RINT1	ENST00000257700.7 link	c.2067+13A>C		intron_variant	Intron 13 of 14	1	NM_021930.6	ENSP00000257700.2		Q6NUQ1
EFCAB10	ENST00000480514.6 link	c.384-23T>G		intron_variant	Intron 4 of 4	1	NM_001355526.2	ENSP00000418678.1		A6NFE3

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15839

AN:

152126

Hom.:

1201

Cov.:

show subpopulations

Gnomad AFR

AF:

0.211

Gnomad AMI

AF:

0.0396

Gnomad AMR

AF:

0.0873

Gnomad ASJ

AF:

0.0585

Gnomad EAS

AF:

0.0896

Gnomad SAS

AF:

0.0865

Gnomad FIN

AF:

0.0605

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0560

Gnomad OTH

AF:

0.0833

GnomAD2 exomes

AF:

0.0796

AC:

19970

AN:

250976

AF XY:

0.0768

show subpopulations

Gnomad AFR exome

AF:

0.215

Gnomad AMR exome

AF:

0.0909

Gnomad ASJ exome

AF:

0.0658

Gnomad EAS exome

AF:

0.101

Gnomad FIN exome

AF:

0.0578

Gnomad NFE exome

AF:

0.0562

Gnomad OTH exome

AF:

0.0645

GnomAD4 exome

AF:

0.0640

AC:

93481

AN:

1459978

Hom.:

3553

Cov.:

AF XY:

0.0644

AC XY:

46775

AN XY:

726110

show subpopulations

African (AFR)

AF:

0.218

AC:

7278

AN:

33394

American (AMR)

AF:

0.0907

AC:

4048

AN:

44630

Ashkenazi Jewish (ASJ)

AF:

0.0640

AC:

1672

AN:

26116

East Asian (EAS)

AF:

0.0825

AC:

3273

AN:

39650

South Asian (SAS)

AF:

0.0880

AC:

7585

AN:

86212

European-Finnish (FIN)

AF:

0.0600

AC:

3204

AN:

53404

Middle Eastern (MID)

AF:

0.0618

AC:

356

AN:

5760

European-Non Finnish (NFE)

AF:

0.0556

AC:

61780

AN:

1110484

Other (OTH)

AF:

0.0710

AC:

4285

AN:

60328

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

4533

9065

13598

18130

22663

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.104

AC:

15880

AN:

152244

Hom.:

1208

Cov.:

AF XY:

0.105

AC XY:

7837

AN XY:

74468

show subpopulations

African (AFR)

AF:

0.211

AC:

8778

AN:

41526

American (AMR)

AF:

0.0877

AC:

1341

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0585

AC:

203

AN:

3468

East Asian (EAS)

AF:

0.0897

AC:

465

AN:

5186

South Asian (SAS)

AF:

0.0858

AC:

414

AN:

4826

European-Finnish (FIN)

AF:

0.0605

AC:

642

AN:

10612

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0560

AC:

3810

AN:

68028

Other (OTH)

AF:

0.0834

AC:

176

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

699

1398

2098

2797

3496

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0721

Hom.:

2279

Bravo

AF:

0.111

Asia WGS

AF:

0.104

AC:

360

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Infantile liver failure syndrome 3

Benign:1

Nov 07, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

-0.28

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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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rs864687

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over