11-113470669-T-C

Variant summary

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

The NM_000795.4(DRD2):​c.-32+4407A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,242 control chromosomes in the GnomAD database, including 2,490 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 0.17 ( 2490 hom., cov: 33)

Consequence

DRD2
NM_000795.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.236
Variant links:
Genes affected
DRD2 (HGNC:3023): (dopamine receptor D2) This gene encodes the D2 subtype of the dopamine receptor. This G-protein coupled receptor inhibits adenylyl cyclase activity. A missense mutation in this gene causes myoclonus dystonia; other mutations have been associated with schizophrenia. Alternative splicing of this gene results in two transcript variants encoding different isoforms. A third variant has been described, but it has not been determined whether this form is normal or due to aberrant splicing. [provided by RefSeq, Jul 2008]

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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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DRD2NM_000795.4 linkuse as main transcriptc.-32+4407A>G intron_variant ENST00000362072.8 NP_000786.1
DRD2NM_016574.4 linkuse as main transcriptc.-32+4407A>G intron_variant NP_057658.2
DRD2XM_017017296.3 linkuse as main transcriptc.-32+3561A>G intron_variant XP_016872785.1
DRD2XM_047426511.1 linkuse as main transcriptc.-32+3561A>G intron_variant XP_047282467.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DRD2ENST00000362072.8 linkuse as main transcriptc.-32+4407A>G intron_variant 1 NM_000795.4 ENSP00000354859 P4P14416-1
DRD2ENST00000346454.7 linkuse as main transcriptc.-32+4407A>G intron_variant 1 ENSP00000278597 P14416-2
DRD2ENST00000540600.5 linkuse as main transcriptn.34+4989A>G intron_variant, non_coding_transcript_variant 1
DRD2ENST00000542616.1 linkuse as main transcriptc.-32+3561A>G intron_variant 4 ENSP00000441474

Frequencies

GnomAD3 genomes
AF:
0.167
AC:
25386
AN:
152124
Hom.:
2480
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.127
Gnomad AMI
AF:
0.236
Gnomad AMR
AF:
0.267
Gnomad ASJ
AF:
0.138
Gnomad EAS
AF:
0.389
Gnomad SAS
AF:
0.184
Gnomad FIN
AF:
0.222
Gnomad MID
AF:
0.180
Gnomad NFE
AF:
0.142
Gnomad OTH
AF:
0.164
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.167
AC:
25429
AN:
152242
Hom.:
2490
Cov.:
33
AF XY:
0.174
AC XY:
12947
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.128
Gnomad4 AMR
AF:
0.268
Gnomad4 ASJ
AF:
0.138
Gnomad4 EAS
AF:
0.390
Gnomad4 SAS
AF:
0.184
Gnomad4 FIN
AF:
0.222
Gnomad4 NFE
AF:
0.142
Gnomad4 OTH
AF:
0.165
Alfa
AF:
0.147
Hom.:
956
Bravo
AF:
0.171
Asia WGS
AF:
0.276
AC:
956
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
3.1
DANN
Benign
0.51

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: rs4938019; hg19: chr11-113341391; API