chr10-102403812-G-A

Variant names:

• chr10-102403812-G-A
• rs11191283
• NM_002779.5:c.2844+30C>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.2844+30C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 1,599,232 control chromosomes in the GnomAD database, including 90,025 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 0.27 (6657 hom., cov: 33)
  • Exomes 𝑓: 0.33 (83368 hom.)
• Consequence: PSD NM_002779.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.822
• Publications: 6 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.428 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.2844+30C>T		intron	N/A	NP_002770.3
	PSD	NM_001270965.2		c.2844+30C>T		intron	N/A	NP_001257894.1
	PSD	NM_001270966.2		c.1707+30C>T		intron	N/A	NP_001257895.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSD	ENST00000020673.6	TSL:1 MANE Select	c.2844+30C>T		intron	N/A	ENSP00000020673.5
	PSD	ENST00000406432.5	TSL:1	c.2844+30C>T		intron	N/A	ENSP00000384830.1
	PSD	ENST00000611678.4	TSL:1	c.1707+30C>T		intron	N/A	ENSP00000481250.1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41288 AN: 151964 Hom.: 6658 Cov.: 33

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.314

GnomAD2 exomes AF: 0.334 AC: 78901 AN: 236582 AF XY: 0.343

Gnomad AFR exome AF: 0.0844

Gnomad AMR exome AF: 0.393

Gnomad ASJ exome AF: 0.350

Gnomad EAS exome AF: 0.190

Gnomad FIN exome AF: 0.335

Gnomad NFE exome AF: 0.342

Gnomad OTH exome AF: 0.346

GnomAD4 exome AF: 0.334 AC: 482988 AN: 1447150 Hom.: 83368 Cov.: 34 AF XY: 0.338 AC XY: 242955 AN XY: 718180

African (AFR) AF: 0.0817 AC: 2724 AN: 33336

American (AMR) AF: 0.387 AC: 16877 AN: 43650

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 8721 AN: 25076

East Asian (EAS) AF: 0.230 AC: 9093 AN: 39502

South Asian (SAS) AF: 0.453 AC: 38188 AN: 84342

European-Finnish (FIN) AF: 0.339 AC: 17827 AN: 52588

Middle Eastern (MID) AF: 0.431 AC: 2457 AN: 5702

European-Non Finnish (NFE) AF: 0.333 AC: 367832 AN: 1103256

Other (OTH) AF: 0.323 AC: 19269 AN: 59698

GnomAD4 genome AF: 0.271 AC: 41284 AN: 152082 Hom.: 6657 Cov.: 33 AF XY: 0.275 AC XY: 20471 AN XY: 74340

African (AFR) AF: 0.0896 AC: 3719 AN: 41524

American (AMR) AF: 0.348 AC: 5320 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1171 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1090 AN: 5142

South Asian (SAS) AF: 0.443 AC: 2138 AN: 4822

European-Finnish (FIN) AF: 0.331 AC: 3503 AN: 10572

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23219 AN: 67946

Other (OTH) AF: 0.309 AC: 654 AN: 2114

Alfa AF: 0.290 Hom.: 1500

Bravo AF: 0.264

Asia WGS AF: 0.318 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.5
DANN	Benign	0.75
PhyloP100		0.82
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: rs11191283; hg19: chr10-104163569; COSMIC: COSV50041699; COSMIC: COSV50041699;