rs2299686

chr20-44646360-T-Cchr20-44646360-T-G

Variant summary

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

The NM_000022.4(ADA):c.33+5215A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,090 control chromosomes in the GnomAD database, including 22,063 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 0.53 (22063 hom., cov: 33)
• Consequence: ADA NM_000022.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

Genes affected

ADA (HGNC:186): (adenosine deaminase) This gene encodes an enzyme that catalyzes the hydrolysis of adenosine to inosine in the purine catabolic pathway. Various mutations have been described for this gene and have been linked to human diseases related to impaired immune function such as severe combined immunodeficiency disease (SCID) which is the result of a deficiency in the ADA enzyme. In ADA-deficient individuals there is a marked depletion of T, B, and NK lymphocytes, and consequently, a lack of both humoral and cellular immunity. Conversely, elevated levels of this enzyme are associated with congenital hemolytic anemia. [provided by RefSeq, Sep 2019]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADA	NM_000022.4	c.33+5215A>G		intron_variant		ENST00000372874.9
ADA	NM_001322050.2	c.-257+5215A>G		intron_variant
ADA	NM_001322051.2	c.33+5215A>G		intron_variant
ADA	NR_136160.2	n.125+5215A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADA	ENST00000372874.9	c.33+5215A>G		intron_variant		1	NM_000022.4	P4

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80461 AN: 151972 Hom.: 22050 Cov.: 33

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.529 AC: 80513 AN: 152090 Hom.: 22063 Cov.: 33 AF XY: 0.537 AC XY: 39903 AN XY: 74372

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.547

Alfa AF: 0.577 Hom.: 51538

Bravo AF: 0.514

Asia WGS AF: 0.653 AC: 2271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.1
Dann	Benign	0.87

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: rs2299686; hg19: chr20-43275001;