1-154587122-T-C

Position:

• chr1-154587122-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_001111.5(ADAR):​c.3020-759A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,928 control chromosomes in the GnomAD database, including 12,664 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as protective (no stars).

• Frequency: Genomes: 𝑓 0.38 (12664 hom., cov: 32)
• Consequence: ADAR NM_001111.5 intron
• Clinical Significance: protective no assertion criteria provided B:1
• Conservation: PhyloP100: -0.162

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 1-154587122-T-C is Benign according to our data. Variant chr1-154587122-T-C is described in ClinVar as [protective]. Clinvar id is 1342841.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_benign, oryginal submission is: [protective].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAR	NM_001111.5	c.3020-759A>G		intron_variant		ENST00000368474.9	NP_001102.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAR	ENST00000368474.9	c.3020-759A>G		intron_variant		1	NM_001111.5	ENSP00000357459.4

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58391 AN: 151810 Hom.: 12636 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.385 AC: 58464 AN: 151928 Hom.: 12664 Cov.: 32 AF XY: 0.381 AC XY: 28259 AN XY: 74252

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.365

Alfa AF: 0.341 Hom.: 3618

Bravo AF: 0.389

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Significance: protective

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Colorectal cancer Benign:1

protective, no assertion criteria provided

case-control

Colorectal Cancer Research Lab, Singapore General Hospital

Mar 01, 2022

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.66

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: rs2131902; hg19: chr1-154559598;