rs3217123

Variant names:

• chr16-8781189-TGATGGATGGATGGATG-T
• rs3217123
• NM_020686.6:c.1382-107_1382-92delGATGGATGGATGGATG

Your query was ambiguous. Multiple possible variants found:

• chr16-8781189-TGATGGATGGATGGATG-T
• chr16-8781189-TGATGGATGGATGGATG-TGATG
• chr16-8781189-TGATGGATGGATGGATG-TGATGGATG
• chr16-8781189-TGATGGATGGATGGATG-TGATGGATGGATG
• chr16-8781189-TGATGGATGGATGGATG-TGATGGATGGATGGATGGATG
• chr16-8781189-TGATGGATGGATGGATG-TGATGGATGGATGGATGGATGGATG
• chr16-8781189-TGATGGATGGATGGATG-TGATGGATGGATGGATGGATGGATGGATG

Variant summary

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

The NM_020686.6(ABAT):​c.1382-107_1382-92delGATGGATGGATGGATG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000702 in 1,281,362 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000070 (0 hom.)
• Consequence: ABAT NM_020686.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

Genes affected

ABAT (HGNC:23): (4-aminobutyrate aminotransferase) 4-aminobutyrate aminotransferase (ABAT) is responsible for catabolism of gamma-aminobutyric acid (GABA), an important, mostly inhibitory neurotransmitter in the central nervous system, into succinic semialdehyde. The active enzyme is a homodimer of 50-kD subunits complexed to pyridoxal-5-phosphate. The protein sequence is over 95% similar to the pig protein. GABA is estimated to be present in nearly one-third of human synapses. ABAT in liver and brain is controlled by 2 codominant alleles with a frequency in a Caucasian population of 0.56 and 0.44. The ABAT deficiency phenotype includes psychomotor retardation, hypotonia, hyperreflexia, lethargy, refractory seizures, and EEG abnormalities. Multiple alternatively spliced transcript variants encoding the same protein isoform have been found for this gene. [provided by RefSeq, Jul 2008]

TMEM186 (HGNC:24530): (transmembrane protein 186) This gene encodes a potential transmembrane protein. [provided by RefSeq, Dec 2012]

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
ABAT	NM_020686.6	c.1382-107_1382-92delGATGGATGGATGGATG		intron_variant	Intron 15 of 15	ENST00000268251.13	NP_065737.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABAT	ENST00000268251.13	c.1382-119_1382-104delGATGGATGGATGGATG		intron_variant	Intron 15 of 15	1	NM_020686.6	ENSP00000268251.8

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000702 AC: 9 AN: 1281362 Hom.: 0 AF XY: 0.00000309 AC XY: 2 AN XY: 646390

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000676

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000630

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

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

LitVar

Other links and lift over

dbSNP: rs3217123; hg19: chr16-8875046;