Variant chr1-154582475-A-AGGGGCATG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001111.5(ADAR):c.*2330_*2331insCATGCCCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.94 ( 66920 hom., cov: 0)

Exomes 𝑓: 1.0 ( 9 hom. )

Consequence

ADAR
NM_001111.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: -0.745

Variant links:

Genes affected

ADAR (HGNC:225): (adenosine deaminase RNA specific) This gene encodes the enzyme responsible for RNA editing by site-specific deamination of adenosines. This enzyme destabilizes double-stranded RNA through conversion of adenosine to inosine. Mutations in this gene have been associated with dyschromatosis symmetrica hereditaria. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]

ADAR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAR	NM_001111.5 linkuse as main transcript	c.2330_2331insCATGCCCC		3_prime_UTR_variant	15/15	ENST00000368474.9	NP_001102.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAR	ENST00000368474.9 linkuse as main transcript	c.2330_2331insCATGCCCC		3_prime_UTR_variant	15/15	1	NM_001111.5	ENSP00000357459	P3	P55265-1

Frequencies

GnomAD3 genomes

AF:

0.935

AC:

141642

AN:

151480

Hom.:

66873

Cov.:

show subpopulations

Gnomad AFR

AF:

0.783

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.974

Gnomad ASJ

AF:

0.999

Gnomad EAS

AF:

0.983

Gnomad SAS

AF:

0.996

Gnomad FIN

AF:

0.999

Gnomad MID

AF:

0.991

Gnomad NFE

AF:

0.996

Gnomad OTH

AF:

0.953

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

Cov.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.935

AC:

141747

AN:

151600

Hom.:

66920

Cov.:

AF XY:

0.937

AC XY:

69425

AN XY:

74084

show subpopulations

Gnomad4 AFR

AF:

0.783

Gnomad4 AMR

AF:

0.974

Gnomad4 ASJ

AF:

0.999

Gnomad4 EAS

AF:

0.983

Gnomad4 SAS

AF:

0.996

Gnomad4 FIN

AF:

0.999

Gnomad4 NFE

AF:

0.996

Gnomad4 OTH

AF:

0.953

Alfa

AF:

0.964

Hom.:

2230

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Symmetrical dyschromatosis of extremities

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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