Variant rs864687 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000257700.7(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
ENST00000257700.7 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.279

Variant links:

Genes affected

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:

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
EFCAB10	NM_001355526.2 linkuse as main transcript	c.*-23T>G		intron_variant		ENST00000480514.6	NP_001342455.1
RINT1	NM_021930.6 linkuse as main transcript	c.2067+13A>C		intron_variant		ENST00000257700.7	NP_068749.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RINT1	ENST00000257700.7 linkuse as main transcript	c.2067+13A>C		intron_variant		1	NM_021930.6	ENSP00000257700	P1
EFCAB10	ENST00000480514.6 linkuse as main transcript	c.*-23T>G		intron_variant		1	NM_001355526.2	ENSP00000418678	A2

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

GnomAD3 exomes

AF:

0.0796

AC:

19970

AN:

250976

Hom.:

994

AF XY:

0.0768

AC XY:

10423

AN XY:

135686

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 SAS exome

AF:

0.0918

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

Gnomad4 AFR exome

AF:

0.218

Gnomad4 AMR exome

AF:

0.0907

Gnomad4 ASJ exome

AF:

0.0640

Gnomad4 EAS exome

AF:

0.0825

Gnomad4 SAS exome

AF:

0.0880

Gnomad4 FIN exome

AF:

0.0600

Gnomad4 NFE exome

AF:

0.0556

Gnomad4 OTH exome

AF:

0.0710

GnomAD4 genome

AF:

0.104

AC:

15880

AN:

152244

Hom.:

1208

Cov.:

AF XY:

0.105

AC XY:

7837

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.211

Gnomad4 AMR

AF:

0.0877

Gnomad4 ASJ

AF:

0.0585

Gnomad4 EAS

AF:

0.0897

Gnomad4 SAS

AF:

0.0858

Gnomad4 FIN

AF:

0.0605

Gnomad4 NFE

AF:

0.0560

Gnomad4 OTH

AF:

0.0834

Alfa

AF:

0.0656

Hom.:

758

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

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

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

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Nov 07, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over