chr3-98799701-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_080927.4(DCBLD2):c.1999G>A(p.Ala667Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,613,874 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080927.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCBLD2 | NM_080927.4 | c.1999G>A | p.Ala667Thr | missense_variant | Exon 16 of 16 | ENST00000326840.11 | NP_563615.3 | |
DCBLD2 | XM_011512419.3 | c.1771G>A | p.Ala591Thr | missense_variant | Exon 15 of 15 | XP_011510721.1 | ||
DCBLD2 | XM_024453348.2 | c.1681G>A | p.Ala561Thr | missense_variant | Exon 16 of 16 | XP_024309116.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCBLD2 | ENST00000326840.11 | c.1999G>A | p.Ala667Thr | missense_variant | Exon 16 of 16 | 1 | NM_080927.4 | ENSP00000321573.6 | ||
DCBLD2 | ENST00000326857.9 | c.2041G>A | p.Ala681Thr | missense_variant | Exon 16 of 16 | 1 | ENSP00000321646.9 | |||
ST3GAL6 | ENST00000491912.1 | n.254-1721C>T | intron_variant | Intron 2 of 3 | 3 | |||||
DCBLD2 | ENST00000496736.1 | n.*135G>A | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248628Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134874
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461684Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727130
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1999G>A (p.A667T) alteration is located in exon 16 (coding exon 16) of the DCBLD2 gene. This alteration results from a G to A substitution at nucleotide position 1999, causing the alanine (A) at amino acid position 667 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at