rs311683

Variant names:

• chr6-73417218-G-A
• rs311683
• NM_018665.3:c.*57G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-73417218-G-A
• chr6-73417218-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018665.3(DDX43):​c.*57G>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 0.488 in 151,900 control chromosomes in the GnomAD database, including 18,729 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 0.49 (18729 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: DDX43 NM_018665.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 13 publications found

Genes affected

DDX43 (HGNC:18677): (DEAD-box helicase 43) The protein encoded by this gene is an ATP-dependent RNA helicase in the DEAD-box family and displays tumor-specific expression. [provided by RefSeq, Jul 2008]

CGAS (HGNC:21367): (cyclic GMP-AMP synthase) Enables several functions, including 2',3'-cyclic GMP-AMP synthase activity; chromatin binding activity; and phosphatidylinositol-4,5-bisphosphate binding activity. Involved in several processes, including cellular response to exogenous dsRNA; positive regulation of intracellular signal transduction; and regulation of defense response. Located in several cellular components, including cytosol; nucleus; and site of double-strand break. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018665.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX43	NM_018665.3	MANE Select	c.*57G>A		3_prime_UTR	Exon 17 of 17	NP_061135.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX43	ENST00000370336.5	TSL:1 MANE Select	c.*57G>A		3_prime_UTR	Exon 17 of 17	ENSP00000359361.4
	CGAS	ENST00000370318.5	TSL:1	c.1333-3197C>T		intron	N/A	ENSP00000359342.1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74063 AN: 151782 Hom.: 18733 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.499

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.488 AC: 74084 AN: 151900 Hom.: 18729 Cov.: 32 AF XY: 0.492 AC XY: 36526 AN XY: 74192

African (AFR) AF: 0.357 AC: 14775 AN: 41414

American (AMR) AF: 0.464 AC: 7087 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1627 AN: 3464

East Asian (EAS) AF: 0.542 AC: 2806 AN: 5178

South Asian (SAS) AF: 0.602 AC: 2897 AN: 4814

European-Finnish (FIN) AF: 0.544 AC: 5717 AN: 10500

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37615 AN: 67960

Other (OTH) AF: 0.503 AC: 1060 AN: 2108

Alfa AF: 0.519 Hom.: 27884

Bravo AF: 0.472

Asia WGS AF: 0.532 AC: 1852 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs311683; hg19: chr6-74126941;