Variant chr6-106572119-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_032730.5(RTN4IP1):c.1084-16C>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 1,582,394 control chromosomes in the GnomAD database, including 12,959 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 2461 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10498 hom. )

Consequence

RTN4IP1
NM_032730.5 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0970

Variant links:

Genes affected

RTN4IP1 (HGNC:18647): (reticulon 4 interacting protein 1) This gene encodes a mitochondrial protein that interacts with reticulon 4, which is a potent inhibitor of regeneration following spinal cord injury. This interaction may be important for reticulon-induced inhibition of neurite growth. Mutations in this gene can cause optic atrophy 10, with or without ataxia, cognitive disability, and seizures. There is a pseudogene for this gene on chromosome 12. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

RTN4IP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 6-106572119-G-T is Benign according to our data. Variant chr6-106572119-G-T is described in ClinVar as [Benign]. Clinvar id is 1168415.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
RTN4IP1	NM_032730.5 linkuse as main transcript	c.1084-16C>A	splice_polypyrimidine_tract_variant, intron_variant	ENST00000369063.8
RTN4IP1	NM_001318746.1 linkuse as main transcript	c.784-16C>A	splice_polypyrimidine_tract_variant, intron_variant
RTN4IP1	XM_011536192.3 linkuse as main transcript	c.844-16C>A	splice_polypyrimidine_tract_variant, intron_variant
RTN4IP1	XM_017011376.3 linkuse as main transcript	c.*33-16C>A	splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
RTN4IP1	ENST00000369063.8 linkuse as main transcript	c.1084-16C>A	splice_polypyrimidine_tract_variant, intron_variant	1	NM_032730.5	P1	Q8WWV3-1
RTN4IP1	ENST00000539449.2 linkuse as main transcript	c.*33-16C>A	splice_polypyrimidine_tract_variant, intron_variant	2
RTN4IP1	ENST00000493619.1 linkuse as main transcript	n.82-16C>A	splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant	3
RTN4IP1	ENST00000498091.1 linkuse as main transcript	n.305-16C>A	splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24726

AN:

152046

Hom.:

2459

Cov.:

show subpopulations

Gnomad AFR

AF:

0.282

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.164

GnomAD3 exomes

AF:

0.130

AC:

31876

AN:

245690

Hom.:

2301

AF XY:

0.128

AC XY:

17092

AN XY:

133064

show subpopulations

Gnomad AFR exome

AF:

0.287

Gnomad AMR exome

AF:

0.111

Gnomad ASJ exome

AF:

0.130

Gnomad EAS exome

AF:

0.131

Gnomad SAS exome

AF:

0.138

Gnomad FIN exome

AF:

0.116

Gnomad NFE exome

AF:

0.113

Gnomad OTH exome

AF:

0.132

GnomAD4 exome

AF:

0.117

AC:

167735

AN:

1430230

Hom.:

10498

Cov.:

AF XY:

0.117

AC XY:

83688

AN XY:

713168

show subpopulations

Gnomad4 AFR exome

AF:

0.287

Gnomad4 AMR exome

AF:

0.114

Gnomad4 ASJ exome

AF:

0.128

Gnomad4 EAS exome

AF:

0.144

Gnomad4 SAS exome

AF:

0.135

Gnomad4 FIN exome

AF:

0.112

Gnomad4 NFE exome

AF:

0.109

Gnomad4 OTH exome

AF:

0.128

GnomAD4 genome

AF:

0.163

AC:

24733

AN:

152164

Hom.:

2461

Cov.:

AF XY:

0.161

AC XY:

12006

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.281

Gnomad4 AMR

AF:

0.131

Gnomad4 ASJ

AF:

0.127

Gnomad4 EAS

AF:

0.142

Gnomad4 SAS

AF:

0.133

Gnomad4 FIN

AF:

0.123

Gnomad4 NFE

AF:

0.110

Gnomad4 OTH

AF:

0.163

Alfa

AF:

0.139

Hom.:

349

Bravo

AF:

0.169

Asia WGS

AF:

0.155

AC:

542

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

9.4

DANN

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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