Variant chr9-5720172-C-G 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_020829.4(RIC1):c.441-10C>G 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 0.449 in 1,597,458 control chromosomes in the GnomAD database, including 170,450 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 14109 hom., cov: 32)

Exomes 𝑓: 0.45 ( 156341 hom. )

Consequence

RIC1
NM_020829.4 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.001624

Clinical Significance

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

Conservation

PhyloP100: 1.33

Variant links:

Genes affected

RIC1 (HGNC:17686): (RIC1 homolog, RAB6A GEF complex partner 1) Enables guanyl-nucleotide exchange factor activity and small GTPase binding activity. Involved in several processes, including positive regulation of GTPase activity; regulation of extracellular matrix constituent secretion; and retrograde transport, endosome to Golgi. Located in cytosol and membrane. Part of Ric1-Rgp1 guanyl-nucleotide exchange factor complex. [provided by Alliance of Genome Resources, Apr 2022]

RIC1 links:

LOC124902115 (HGNC:):

LOC124902115 links:

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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 9-5720172-C-G is Benign according to our data. Variant chr9-5720172-C-G is described in ClinVar as [Benign]. Clinvar id is 1300068.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RIC1	NM_020829.4 linkuse as main transcript	c.441-10C>G		splice_polypyrimidine_tract_variant, intron_variant		ENST00000414202.7
LOC124902115	XR_007061409.1 linkuse as main transcript	n.15G>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RIC1	ENST00000414202.7 linkuse as main transcript	c.441-10C>G		splice_polypyrimidine_tract_variant, intron_variant		5	NM_020829.4	P1	Q4ADV7-1
	ENST00000426764.1 linkuse as main transcript	n.65+8G>C		splice_region_variant, intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.404

AC:

61347

AN:

151960

Hom.:

14101

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.374

Gnomad AMR

AF:

0.488

Gnomad ASJ

AF:

0.435

Gnomad EAS

AF:

0.872

Gnomad SAS

AF:

0.608

Gnomad FIN

AF:

0.501

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.436

Gnomad OTH

AF:

0.402

GnomAD3 exomes

AF:

0.502

AC:

125053

AN:

249244

Hom.:

33994

AF XY:

0.505

AC XY:

68000

AN XY:

134664

show subpopulations

Gnomad AFR exome

AF:

0.204

Gnomad AMR exome

AF:

0.558

Gnomad ASJ exome

AF:

0.446

Gnomad EAS exome

AF:

0.882

Gnomad SAS exome

AF:

0.592

Gnomad FIN exome

AF:

0.507

Gnomad NFE exome

AF:

0.447

Gnomad OTH exome

AF:

0.480

GnomAD4 exome

AF:

0.454

AC:

656630

AN:

1445380

Hom.:

156341

Cov.:

AF XY:

0.459

AC XY:

330248

AN XY:

719876

show subpopulations

Gnomad4 AFR exome

AF:

0.194

Gnomad4 AMR exome

AF:

0.548

Gnomad4 ASJ exome

AF:

0.439

Gnomad4 EAS exome

AF:

0.871

Gnomad4 SAS exome

AF:

0.586

Gnomad4 FIN exome

AF:

0.509

Gnomad4 NFE exome

AF:

0.431

Gnomad4 OTH exome

AF:

0.457

GnomAD4 genome

AF:

0.404

AC:

61368

AN:

152078

Hom.:

14109

Cov.:

AF XY:

0.415

AC XY:

30845

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.209

Gnomad4 AMR

AF:

0.489

Gnomad4 ASJ

AF:

0.435

Gnomad4 EAS

AF:

0.871

Gnomad4 SAS

AF:

0.608

Gnomad4 FIN

AF:

0.501

Gnomad4 NFE

AF:

0.436

Gnomad4 OTH

AF:

0.409

Alfa

AF:

0.432

Hom.:

2835

Bravo

AF:

0.393

Asia WGS

AF:

0.695

AC:

2413

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Catifa syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

6.9

DANN

Benign

0.75

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0016

dbscSNV1_RF

Benign

0.11

SpliceAI score (max)

0.070

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