rs828621
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_080927.4(DCBLD2):c.623+497A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,810 control chromosomes in the GnomAD database, including 11,010 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 0.36 ( 11010 hom., cov: 31)
Consequence
DCBLD2
NM_080927.4 intron
NM_080927.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.702
Genes affected
DCBLD2 (HGNC:24627): (discoidin, CUB and LCCL domain containing 2) Involved in negative regulation of cell growth and wound healing. Located in cell surface. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCBLD2 | NM_080927.4 | c.623+497A>T | intron_variant | ENST00000326840.11 | NP_563615.3 | |||
DCBLD2 | XM_011512419.3 | c.395+497A>T | intron_variant | XP_011510721.1 | ||||
DCBLD2 | XM_024453348.2 | c.305+497A>T | intron_variant | XP_024309116.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCBLD2 | ENST00000326840.11 | c.623+497A>T | intron_variant | 1 | NM_080927.4 | ENSP00000321573.6 | ||||
DCBLD2 | ENST00000326857.9 | c.623+497A>T | intron_variant | 1 | ENSP00000321646.9 | |||||
DCBLD2 | ENST00000469648.5 | n.458+497A>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.361 AC: 54754AN: 151692Hom.: 11004 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.361 AC: 54772AN: 151810Hom.: 11010 Cov.: 31 AF XY: 0.366 AC XY: 27161AN XY: 74174
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at