chr10-102403013-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002779.5(PSD):​c.*187C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 309,338 control chromosomes in the GnomAD database, including 19,644 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 0.31 (7011 hom., cov: 28)
  • Exomes 𝑓: 0.44 (12633 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

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>T		3_prime_UTR	Exon 17 of 17	NP_002770.3
	PSD	NR_073110.2		n.1554C>T		non_coding_transcript_exon	Exon 8 of 8
	PSD	NM_001270965.2		c.*187C>T		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>T		3_prime_UTR	Exon 17 of 17	ENSP00000020673.5
	PSD	ENST00000406432.5	TSL:1	c.*187C>T		3_prime_UTR	Exon 18 of 18	ENSP00000384830.1
	PSD	ENST00000611678.4	TSL:1	c.*187C>T		3_prime_UTR	Exon 18 of 18	ENSP00000481250.1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 43820 AN: 140728 Hom.: 7011 Cov.: 28

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.346

GnomAD4 exome AF: 0.441 AC: 74269 AN: 168544 Hom.: 12633 Cov.: 4 AF XY: 0.444 AC XY: 38279 AN XY: 86244

African (AFR) AF: 0.278 AC: 979 AN: 3522

American (AMR) AF: 0.473 AC: 2372 AN: 5020

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 2775 AN: 6026

East Asian (EAS) AF: 0.359 AC: 5177 AN: 14440

South Asian (SAS) AF: 0.549 AC: 1582 AN: 2884

European-Finnish (FIN) AF: 0.433 AC: 6787 AN: 15680

Middle Eastern (MID) AF: 0.536 AC: 495 AN: 924

European-Non Finnish (NFE) AF: 0.451 AC: 49328 AN: 109274

Other (OTH) AF: 0.443 AC: 4774 AN: 10774

GnomAD4 genome AF: 0.311 AC: 43818 AN: 140794 Hom.: 7011 Cov.: 28 AF XY: 0.319 AC XY: 21688 AN XY: 68086

African (AFR) AF: 0.173 AC: 6258 AN: 36234

American (AMR) AF: 0.395 AC: 5391 AN: 13656

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1138 AN: 3434

East Asian (EAS) AF: 0.236 AC: 1071 AN: 4538

South Asian (SAS) AF: 0.497 AC: 2264 AN: 4556

European-Finnish (FIN) AF: 0.388 AC: 3427 AN: 8840

Middle Eastern (MID) AF: 0.430 AC: 122 AN: 284

European-Non Finnish (NFE) AF: 0.348 AC: 23121 AN: 66384

Other (OTH) AF: 0.342 AC: 677 AN: 1978

Alfa AF: 0.333 Hom.: 14810

Bravo AF: 0.285

Asia WGS AF: 0.336 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.15
DANN	Benign	0.90
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

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;