chr6-165876668-G-A

Variant summary

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

The ENST00000647768.3(PDE10A):​c.106+109440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,118 control chromosomes in the GnomAD database, including 45,263 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 0.77 ( 45263 hom., cov: 32)

Consequence

PDE10A
ENST00000647768.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0810
Variant links:
Genes affected
PDE10A (HGNC:8772): (phosphodiesterase 10A) The protein encoded by this gene belongs to the cyclic nucleotide phosphodiesterase family. It plays a role in signal transduction by regulating the intracellular concentration of cyclic nucleotides. This protein can hydrolyze both cAMP and cGMP to the corresponding nucleoside 5' monophosphate, but has higher affinity for cAMP, and is more efficient with cAMP as substrate. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Dec 2011]

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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PDE10AXM_011535387.4 linkuse as main transcriptc.58+34140C>T intron_variant XP_011533689.2
PDE10AXM_017010194.3 linkuse as main transcriptc.58+34140C>T intron_variant XP_016865683.1
PDE10AXM_017010197.3 linkuse as main transcriptc.58+34140C>T intron_variant XP_016865686.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PDE10AENST00000366882.7 linkuse as main transcriptc.-615+110861C>T intron_variant 5 ENSP00000355847
PDE10AENST00000647768.3 linkuse as main transcriptc.106+109440C>T intron_variant ENSP00000497930 A2
PDE10AENST00000672859.1 linkuse as main transcriptc.-308-84333C>T intron_variant ENSP00000500900 A2

Frequencies

GnomAD3 genomes
AF:
0.769
AC:
116954
AN:
152000
Hom.:
45221
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.754
Gnomad AMI
AF:
0.862
Gnomad AMR
AF:
0.798
Gnomad ASJ
AF:
0.733
Gnomad EAS
AF:
0.960
Gnomad SAS
AF:
0.878
Gnomad FIN
AF:
0.803
Gnomad MID
AF:
0.744
Gnomad NFE
AF:
0.746
Gnomad OTH
AF:
0.771
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.769
AC:
117049
AN:
152118
Hom.:
45263
Cov.:
32
AF XY:
0.777
AC XY:
57755
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.754
Gnomad4 AMR
AF:
0.798
Gnomad4 ASJ
AF:
0.733
Gnomad4 EAS
AF:
0.960
Gnomad4 SAS
AF:
0.877
Gnomad4 FIN
AF:
0.803
Gnomad4 NFE
AF:
0.746
Gnomad4 OTH
AF:
0.774
Alfa
AF:
0.758
Hom.:
12154
Bravo
AF:
0.769
Asia WGS
AF:
0.921
AC:
3201
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.26
DANN
Benign
0.63

Splicing

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: rs3002430; hg19: chr6-166290156; API