GeneBe

chr3-98824818-T-C

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_080927.4(DCBLD2):​c.623+497A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000659 in 151,768 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 31)

Consequence

DCBLD2
NM_080927.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.702

Publications

4 publications found
Variant links:
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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DCBLD2NM_080927.4 linkc.623+497A>G intron_variant Intron 4 of 15 ENST00000326840.11 NP_563615.3 Q96PD2-1
DCBLD2XM_011512419.3 linkc.395+497A>G intron_variant Intron 3 of 14 XP_011510721.1
DCBLD2XM_024453348.2 linkc.305+497A>G intron_variant Intron 4 of 15 XP_024309116.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DCBLD2ENST00000326840.11 linkc.623+497A>G intron_variant Intron 4 of 15 1 NM_080927.4 ENSP00000321573.6 Q96PD2-1
DCBLD2ENST00000326857.9 linkc.623+497A>G intron_variant Intron 4 of 15 1 ENSP00000321646.9 Q96PD2-2
DCBLD2ENST00000469648.5 linkn.458+497A>G intron_variant Intron 3 of 4 3

Frequencies

GnomAD3 genomes
AF:
0.00000659
AC:
1
AN:
151768
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000656
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00000659
AC:
1
AN:
151768
Hom.:
0
Cov.:
31
AF XY:
0.0000135
AC XY:
1
AN XY:
74086
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
41308
American (AMR)
AF:
0.0000656
AC:
1
AN:
15236
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3470
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5160
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4816
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10500
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67972
Other (OTH)
AF:
0.00
AC:
0
AN:
2086
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
573

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.19
DANN
Benign
0.66
PhyloP100
-0.70

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

Other links and lift over

dbSNP: rs828621; hg19: chr3-98543662; API