NM_000022.4:c.1079-14_1079-4delGAACCAACGAG

Variant names:

• chr20-44619850-GCTCGTTGGTTC-G
• NM_000022.4:c.1079-14_1079-4delGAACCAACGAG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000022.4(ADA):​c.1079-14_1079-4delGAACCAACGAG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as no classification for the single variant (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ADA NM_000022.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.854

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]

PKIG (HGNC:9019): (cAMP-dependent protein kinase inhibitor gamma) This gene encodes a member of the protein kinase inhibitor family. Studies of a similar protein in mice suggest that this protein acts as a potent competitive cAMP-dependent protein kinase inhibitor, and is a predominant form of inhibitor in various tissues. The encoded protein may be involved in osteogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADA	NM_000022.4	c.1079-14_1079-4delGAACCAACGAG		splice_region_variant, intron_variant	Intron 11 of 11	ENST00000372874.9	NP_000013.2
ADA	NM_001322051.2	c.1007-14_1007-4delGAACCAACGAG		splice_region_variant, intron_variant	Intron 10 of 10		NP_001308980.1
ADA	NM_001322050.2	c.674-14_674-4delGAACCAACGAG		splice_region_variant, intron_variant	Intron 10 of 10		NP_001308979.1
ADA	NR_136160.2	n.1106-14_1106-4delGAACCAACGAG		splice_region_variant, intron_variant	Intron 10 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADA	ENST00000372874.9	c.1079-14_1079-4delGAACCAACGAG		splice_region_variant, intron_variant	Intron 11 of 11	1	NM_000022.4	ENSP00000361965.4
ADA	ENST00000695995.1	c.689-14_689-4delGAACCAACGAG		splice_region_variant, intron_variant	Intron 8 of 8			ENSP00000512318.1
ADA	ENST00000695991.1	c.617-14_617-4delGAACCAACGAG		splice_region_variant, intron_variant	Intron 7 of 7			ENSP00000512314.1
ADA	ENST00000695956.1	c.233-1_242delGAACCAACGAG	p.Glu78fs	frameshift_variant, splice_acceptor_variant, splice_region_variant, intron_variant	Exon 3 of 3			ENSP00000512285.1
ADA	ENST00000696038.1	n.*1273_*1283delGAACCAACGAG		non_coding_transcript_exon_variant	Exon 9 of 9			ENSP00000512344.1
ADA	ENST00000696038.1	n.*1273_*1283delGAACCAACGAG		3_prime_UTR_variant	Exon 9 of 9			ENSP00000512344.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-43248491;