Variant chr7-105551717-T-C 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 NM_021930.6(RINT1):c.1471+10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00545 in 1,579,480 control chromosomes in the GnomAD database, including 350 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.010 ( 57 hom., cov: 32)

Exomes 𝑓: 0.0050 ( 293 hom. )

Consequence

RINT1
NM_021930.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.291

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:

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=-0.83).

BP6

Variant 7-105551717-T-C is Benign according to our data. Variant chr7-105551717-T-C is described in ClinVar as [Benign]. Clinvar id is 416391.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RINT1	NM_021930.6 linkuse as main transcript	c.1471+10T>C		intron_variant		ENST00000257700.7

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
RINT1	ENST00000257700.7 linkuse as main transcript	c.1471+10T>C	intron_variant	1	NM_021930.6	P1
RINT1	ENST00000497979.5 linkuse as main transcript	c.*1076+10T>C	intron_variant, NMD_transcript_variant	5
RINT1	ENST00000474123.1 linkuse as main transcript	n.475+10T>C	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.00987

AC:

1502

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00176

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0640

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.0712

Gnomad SAS

AF:

0.00393

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000441

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.0163

AC:

3663

AN:

224890

Hom.:

157

AF XY:

0.0136

AC XY:

1659

AN XY:

121948

show subpopulations

Gnomad AFR exome

AF:

0.00161

Gnomad AMR exome

AF:

0.0867

Gnomad ASJ exome

AF:

0.000469

Gnomad EAS exome

AF:

0.0719

Gnomad SAS exome

AF:

0.00283

Gnomad FIN exome

AF:

0.0000473

Gnomad NFE exome

AF:

0.000290

Gnomad OTH exome

AF:

0.0136

GnomAD4 exome

AF:

0.00496

AC:

7084

AN:

1427154

Hom.:

293

Cov.:

AF XY:

0.00460

AC XY:

3261

AN XY:

709088

show subpopulations

Gnomad4 AFR exome

AF:

0.00110

Gnomad4 AMR exome

AF:

0.0840

Gnomad4 ASJ exome

AF:

0.000808

Gnomad4 EAS exome

AF:

0.0774

Gnomad4 SAS exome

AF:

0.00293

Gnomad4 FIN exome

AF:

0.0000567

Gnomad4 NFE exome

AF:

0.000217

Gnomad4 OTH exome

AF:

0.00724

GnomAD4 genome

AF:

0.00997

AC:

1518

AN:

152326

Hom.:

Cov.:

AF XY:

0.0114

AC XY:

849

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.00176

Gnomad4 AMR

AF:

0.0648

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.0716

Gnomad4 SAS

AF:

0.00394

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.000441

Gnomad4 OTH

AF:

0.0142

Alfa

AF:

0.00317

Hom.:

Bravo

AF:

0.0148

Asia WGS

AF:

0.0330

AC:

116

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

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	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.9

DANN

Benign

0.55

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

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