rs2279398

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001308236.3(DOK3):​c.*215G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0171 in 1,418,996 control chromosomes in the GnomAD database, including 2,137 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 0.031 ( 333 hom., cov: 33)
Exomes 𝑓: 0.015 ( 1804 hom. )

Consequence

DOK3
NM_001308236.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.00
Variant links:
Genes affected
DOK3 (HGNC:24583): (docking protein 3) Predicted to be involved in Ras protein signal transduction and transmembrane receptor protein tyrosine kinase signaling pathway. Predicted to be located in ficolin-1-rich granule membrane and plasma membrane. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DOK3NM_001308236.3 linkuse as main transcriptc.*215G>A 3_prime_UTR_variant 6/6 ENST00000510898.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DOK3ENST00000510898.7 linkuse as main transcriptc.*215G>A 3_prime_UTR_variant 6/63 NM_001308236.3 P1

Frequencies

GnomAD3 genomes
AF:
0.0308
AC:
4693
AN:
152154
Hom.:
334
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0293
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0728
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.286
Gnomad SAS
AF:
0.0694
Gnomad FIN
AF:
0.0285
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00240
Gnomad OTH
AF:
0.0368
GnomAD4 exome
AF:
0.0154
AC:
19524
AN:
1266724
Hom.:
1804
Cov.:
30
AF XY:
0.0162
AC XY:
9936
AN XY:
612132
show subpopulations
Gnomad4 AFR exome
AF:
0.0295
Gnomad4 AMR exome
AF:
0.0988
Gnomad4 ASJ exome
AF:
0.00150
Gnomad4 EAS exome
AF:
0.297
Gnomad4 SAS exome
AF:
0.0567
Gnomad4 FIN exome
AF:
0.0251
Gnomad4 NFE exome
AF:
0.00129
Gnomad4 OTH exome
AF:
0.0288
GnomAD4 genome
AF:
0.0308
AC:
4696
AN:
152272
Hom.:
333
Cov.:
33
AF XY:
0.0342
AC XY:
2548
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.0293
Gnomad4 AMR
AF:
0.0727
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.287
Gnomad4 SAS
AF:
0.0697
Gnomad4 FIN
AF:
0.0285
Gnomad4 NFE
AF:
0.00240
Gnomad4 OTH
AF:
0.0369
Alfa
AF:
0.0115
Hom.:
86
Bravo
AF:
0.0372
Asia WGS
AF:
0.149
AC:
516
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.13
DANN
Benign
0.60

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2279398; hg19: chr5-176930769; API