rs3738029

Positions:

• chr1-154602845-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001111.5(ADAR):​c.16-219C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,140 control chromosomes in the GnomAD database, including 6,360 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.29 (6360 hom., cov: 33)
• Consequence: ADAR NM_001111.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.566

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 1-154602845-G-A is Benign according to our data. Variant chr1-154602845-G-A is described in ClinVar as [Benign]. Clinvar id is 1275613.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAR	NM_001111.5	c.16-219C>T		intron_variant		ENST00000368474.9	NP_001102.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAR	ENST00000368474.9	c.16-219C>T		intron_variant		1	NM_001111.5	ENSP00000357459.4

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43917 AN: 152022 Hom.: 6343 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.295

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.289 AC: 43970 AN: 152140 Hom.: 6360 Cov.: 33 AF XY: 0.287 AC XY: 21316 AN XY: 74364

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.300

Alfa AF: 0.287 Hom.: 811

Bravo AF: 0.280

Asia WGS AF: 0.280 AC: 972 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 07, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.26

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

Other links and lift over

dbSNP: rs3738029; hg19: chr1-154575321;