19-3769901-C-T

Variant summary

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

The NM_001319074.4(RAX2):c.*720G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 137,626 control chromosomes in the GnomAD database, including 1,836 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.17 ( 1827 hom., cov: 32)

Exomes 𝑓: 0.13 ( 9 hom. )

Consequence

RAX2
NM_001319074.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -0.631

Variant links:

Genes affected

RAX2 (HGNC:18286): (retina and anterior neural fold homeobox 2) This gene encodes a homeodomain-containing protein that plays a role in eye development. Mutation of this gene causes age-related macular degeneration type 6, an eye disorder resulting in accumulations of protein and lipid beneath the retinal pigment epithelium and within the Bruch's membrane. Defects in this gene can also cause cone-rod dystrophy type 11, a disease characterized by the initial degeneration of cone photoreceptor cells and resulting in loss of color vision and visual acuity, followed by the degeneration of rod photoreceptor cells, which progresses to night blindness and the loss of peripheral vision. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

RAX2 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=-0.89).

BP6

Variant 19-3769901-C-T is Benign according to our data. Variant chr19-3769901-C-T is described in ClinVar as [Benign]. Clinvar id is 328955.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAX2	NM_001319074.4 linkuse as main transcript	c.*720G>A		3_prime_UTR_variant	3/3	ENST00000555633.3
RAX2	NM_032753.4 linkuse as main transcript	c.*720G>A		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAX2	ENST00000555633.3 linkuse as main transcript	c.*720G>A		3_prime_UTR_variant	3/3	1	NM_001319074.4	P1
RAX2	ENST00000555978.5 linkuse as main transcript	c.*720G>A		3_prime_UTR_variant	3/3	1		P1

Frequencies

GnomAD3 genomes

AF:

0.165

AC:

22616

AN:

136944

Hom.:

1827

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.146

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.0256

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.161

Gnomad MID

AF:

0.201

Gnomad NFE

AF:

0.182

Gnomad OTH

AF:

0.181

GnomAD4 exome

AF:

0.125

AC:

AN:

568

Hom.:

Cov.:

AF XY:

0.133

AC XY:

AN XY:

420

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0417

Gnomad4 FIN exome

AF:

0.0909

Gnomad4 NFE exome

AF:

0.140

Gnomad4 OTH exome

AF:

0.100

GnomAD4 genome

AF:

0.165

AC:

22635

AN:

137058

Hom.:

1827

Cov.:

AF XY:

0.164

AC XY:

11011

AN XY:

67196

show subpopulations

Gnomad4 AFR

AF:

0.162

Gnomad4 AMR

AF:

0.146

Gnomad4 ASJ

AF:

0.165

Gnomad4 EAS

AF:

0.0256

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.161

Gnomad4 NFE

AF:

0.182

Gnomad4 OTH

AF:

0.180

Alfa

AF:

0.163

Hom.:

245

Bravo

AF:

0.148

Asia WGS

AF:

0.0940

AC:

326

AN:

3446

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Cone-rod dystrophy 11

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Age related macular degeneration 6

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

Cadd

Benign

5.8

Dann

Benign

0.90

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