NM_002779.5:c.*187C>G

Variant names:

• chr10-102403013-G-C
• rs1056890
• NM_002779.5:c.*187C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002779.5(PSD):​c.*187C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 28)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PSD NM_002779.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 53 publications found

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]

ACMG classification

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002779.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSD	NM_002779.5	MANE Select	c.*187C>G		3_prime_UTR	Exon 17 of 17	NP_002770.3
	PSD	NR_073110.2		n.1554C>G		non_coding_transcript_exon	Exon 8 of 8
	PSD	NM_001270965.2		c.*187C>G		3_prime_UTR	Exon 18 of 18	NP_001257894.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSD	ENST00000020673.6	TSL:1 MANE Select	c.*187C>G		3_prime_UTR	Exon 17 of 17	ENSP00000020673.5
	PSD	ENST00000406432.5	TSL:1	c.*187C>G		3_prime_UTR	Exon 18 of 18	ENSP00000384830.1
	PSD	ENST00000611678.4	TSL:1	c.*187C>G		3_prime_UTR	Exon 18 of 18	ENSP00000481250.1

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 169066 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 86488

African (AFR) AF: 0.00 AC: 0 AN: 3528

American (AMR) AF: 0.00 AC: 0 AN: 5028

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6040

East Asian (EAS) AF: 0.00 AC: 0 AN: 14480

South Asian (SAS) AF: 0.00 AC: 0 AN: 2898

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 15734

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 926

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 109626

Other (OTH) AF: 0.00 AC: 0 AN: 10806

GnomAD4 genome Cov.: 28

Alfa AF: 0.00 Hom.: 14810

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.10
DANN	Benign	0.72
PhyloP100		-0.11

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

Other links and lift over

dbSNP: rs1056890; hg19: chr10-104162770;