GeneBe

chr10-102410909-C-G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_002779.5(PSD):​c.2040G>C​(p.Gly680Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,722 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. Synonymous variant affecting the same amino acid position (i.e. G680G) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

PSD
NM_002779.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.268

Publications

0 publications found
Variant links:
Genes affected
PSD (HGNC:9507): (pleckstrin and Sec7 domain containing) This gene encodes a Plekstrin homology and SEC7 domains-containing protein that functions as a guanine nucleotide exchange factor. The encoded protein regulates signal transduction by activating ADP-ribosylation factor 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP7
Synonymous conserved (PhyloP=-0.268 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PSDNM_002779.5 linkc.2040G>C p.Gly680Gly synonymous_variant Exon 10 of 17 ENST00000020673.6 NP_002770.3 A5PKW4-1
PSDNM_001270965.2 linkc.2040G>C p.Gly680Gly synonymous_variant Exon 11 of 18 NP_001257894.1 A5PKW4-1
PSDNM_001270966.2 linkc.903G>C p.Gly301Gly synonymous_variant Exon 11 of 18 NP_001257895.1 A5PKW4-2Q86YI3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PSDENST00000020673.6 linkc.2040G>C p.Gly680Gly synonymous_variant Exon 10 of 17 1 NM_002779.5 ENSP00000020673.5 A5PKW4-1
PSDENST00000406432.5 linkc.2040G>C p.Gly680Gly synonymous_variant Exon 11 of 18 1 ENSP00000384830.1 A5PKW4-1
PSDENST00000611678.4 linkc.903G>C p.Gly301Gly synonymous_variant Exon 11 of 18 1 ENSP00000481250.1 A5PKW4-2
PSDENST00000488194.1 linkn.148G>C non_coding_transcript_exon_variant Exon 3 of 5 3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461722
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
727156
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33474
American (AMR)
AF:
0.00
AC:
0
AN:
44720
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26134
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39700
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86254
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53410
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5742
European-Non Finnish (NFE)
AF:
8.99e-7
AC:
1
AN:
1111908
Other (OTH)
AF:
0.00
AC:
0
AN:
60380
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
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.33
CADD
Benign
10
DANN
Benign
0.81
PhyloP100
-0.27

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: rs1302761895; hg19: chr10-104170666; API