Genetic Variant NM_002779.5:c.2844+30C>T (chr10-102403812-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.822

Publications

6 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]

PSD links:

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ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	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	A5PKW4-1
PSD	NM_001270966.2		c.1707+30C>T	intron	N/A	NP_001257895.1	A5PKW4-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PSD	ENST00000020673.6	TSL:1 MANE Select	c.2844+30C>T	intron	N/A	ENSP00000020673.5	A5PKW4-1
PSD	ENST00000406432.5	TSL:1	c.2844+30C>T	intron	N/A	ENSP00000384830.1	A5PKW4-1
PSD	ENST00000611678.4	TSL:1	c.1707+30C>T	intron	N/A	ENSP00000481250.1	A5PKW4-2

Frequencies

GnomAD3 genomes

AF:

0.272

AC:

41288

AN:

151964

Hom.:

6658

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.338

AC XY:

242955

AN XY:

718180

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

14464

28928

43391

57855

72319

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11842

23684

35526

47368

59210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.271

AC:

41284

AN:

152082

Hom.:

6657

Cov.:

AF XY:

0.275

AC XY:

20471

AN XY:

74340

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1472

2944

4416

5888

7360

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

430

860

1290

1720

2150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.75

PhyloP100

0.82

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over