Genetic Variant NM_014314.4:c.571+37A>G (chr9-32492354-T-C) – ACMG Classification: Benign (-14 pts)

Variant summary

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

The NM_014314.4(RIGI):c.571+37A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 1,610,292 control chromosomes in the GnomAD database, including 14,703 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1143 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13560 hom. )

Consequence

RIGI
NM_014314.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.844

Variant links:

Genes affected

RIGI (HGNC:19102): (RNA sensor RIG-I) DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases which are implicated in a number of cellular processes involving RNA binding and alteration of RNA secondary structure. This gene encodes a protein containing RNA helicase-DEAD box protein motifs and a caspase recruitment domain (CARD). It is involved in viral double-stranded (ds) RNA recognition and the regulation of the antiviral innate immune response. Mutations in this gene are associated with Singleton-Merten syndrome 2. [provided by RefSeq, Aug 2020]

RIGI links:

ENSG00000288684 (HGNC:):

ENSG00000288684 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=-0.97).

BP6

Variant 9-32492354-T-C is Benign according to our data. Variant chr9-32492354-T-C is described in ClinVar as [Benign]. Clinvar id is 2688507.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RIGI	NM_014314.4 link	c.571+37A>G		intron_variant	Intron 4 of 17	ENST00000379883.3	NP_055129.2	O95786-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIGI	ENST00000379883.3 link	c.571+37A>G		intron_variant	Intron 4 of 17	1	NM_014314.4	ENSP00000369213.2		O95786-1
ENSG00000288684	ENST00000681750.1 link	c.421+37A>G		intron_variant	Intron 6 of 19			ENSP00000506413.1		A0A7P0TB70

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17651

AN:

151934

Hom.:

1142

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0721

Gnomad AMI

AF:

0.179

Gnomad AMR

AF:

0.0986

Gnomad ASJ

AF:

0.210

Gnomad EAS

AF:

0.0139

Gnomad SAS

AF:

0.0688

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.148

Gnomad OTH

AF:

0.142

GnomAD3 exomes

AF:

0.114

AC:

28375

AN:

248800

Hom.:

1965

AF XY:

0.116

AC XY:

15672

AN XY:

134530

show subpopulations

Gnomad AFR exome

AF:

0.0683

Gnomad AMR exome

AF:

0.0641

Gnomad ASJ exome

AF:

0.209

Gnomad EAS exome

AF:

0.0103

Gnomad SAS exome

AF:

0.0686

Gnomad FIN exome

AF:

0.140

Gnomad NFE exome

AF:

0.150

Gnomad OTH exome

AF:

0.141

GnomAD4 exome

AF:

0.131

AC:

191697

AN:

1458240

Hom.:

13560

Cov.:

AF XY:

0.131

AC XY:

94911

AN XY:

725292

show subpopulations

Gnomad4 AFR exome

AF:

0.0720

Gnomad4 AMR exome

AF:

0.0697

Gnomad4 ASJ exome

AF:

0.211

Gnomad4 EAS exome

AF:

0.0122

Gnomad4 SAS exome

AF:

0.0734

Gnomad4 FIN exome

AF:

0.138

Gnomad4 NFE exome

AF:

0.142

Gnomad4 OTH exome

AF:

0.132

GnomAD4 genome

AF:

0.116

AC:

17665

AN:

152052

Hom.:

1143

Cov.:

AF XY:

0.114

AC XY:

8465

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.0723

Gnomad4 AMR

AF:

0.0985

Gnomad4 ASJ

AF:

0.210

Gnomad4 EAS

AF:

0.0140

Gnomad4 SAS

AF:

0.0686

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.148

Gnomad4 OTH

AF:

0.142

Alfa

AF:

0.147

Hom.:

1812

Bravo

AF:

0.112

Asia WGS

AF:

0.0730

AC:

256

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 22% of patients studied by a panel of primary immunodeficiencies. Number of patients: 19. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

2.6

DANN

Benign

0.51

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