rs117732387

chr7-105551717-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.291

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]

ACMG classification

Verdict is Benign. Variant got -14 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_single_submitter, 1 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	c.1471+10T>C		intron_variant		ENST00000257700.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RINT1	ENST00000257700.7	c.1471+10T>C		intron_variant		1	NM_021930.6	P1
RINT1	ENST00000497979.5	c.*1076+10T>C		intron_variant, NMD_transcript_variant		5
RINT1	ENST00000474123.1	n.475+10T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00987 AC: 1502 AN: 152208 Hom.: 53 Cov.: 32

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

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.: 27 AF XY: 0.00460 AC XY: 3261 AN XY: 709088

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.: 57 Cov.: 32 AF XY: 0.0114 AC XY: 849 AN XY: 74494

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.: 4

Bravo AF: 0.0148

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

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

Other links and lift over

dbSNP: rs117732387; hg19: chr7-105192164; COSMIC: COSV57559957; COSMIC: COSV57559957;