chr1-154617152-A-C

Position:

• chr1-154617152-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365045.1(ADAR):​c.42+10802T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,128 control chromosomes in the GnomAD database, including 2,812 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2812 hom., cov: 32)
• Consequence: ADAR NM_001365045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAR	NM_001365045.1	c.42+10802T>G		intron_variant			NP_001351974.1
ADAR	NM_001025107.3	c.-871+10703T>G		intron_variant			NP_001020278.1
ADAR	NM_001365046.1	c.-735+10802T>G		intron_variant			NP_001351975.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAR	ENST00000368471.8	c.-871+10703T>G		intron_variant		1		ENSP00000357456.3
ADAR	ENST00000648311.1	c.-871+10284T>G		intron_variant				ENSP00000498137.1
ADAR	ENST00000649022.2	c.-871+7911T>G		intron_variant				ENSP00000496896.2

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27194 AN: 152012 Hom.: 2814 Cov.: 32

Gnomad AFR AF: 0.0841

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.179 AC: 27203 AN: 152128 Hom.: 2812 Cov.: 32 AF XY: 0.182 AC XY: 13512 AN XY: 74356

Gnomad4 AFR AF: 0.0840

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.197

Alfa AF: 0.209 Hom.: 7076

Bravo AF: 0.174

Asia WGS AF: 0.246 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2335230; hg19: chr1-154589628;