Variant rs5924658 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173493.3(PASD1):c.637C>G(p.Gln213Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 1,207,244 control chromosomes in the GnomAD database, including 28,515 homozygotes. There are 100,240 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.20 ( 2041 hom., 6303 hem., cov: 22)

Exomes 𝑓: 0.26 ( 26474 hom. 93937 hem. )

Consequence

PASD1
NM_173493.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.754

Variant links:

Genes affected

PASD1 (HGNC:20686): (PAS domain containing repressor 1) This gene encodes a protein that is thought to function as a transcription factor. The protein is a cancer-associated antigen that can stimulate autologous T-cell responses, and it is therefore considered to be a potential immunotherapeutic target for the treatment of various hematopoietic malignancies, including diffuse large B-cell lymphoma. [provided by RefSeq, May 2010]

PASD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0056649745).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PASD1	NM_173493.3 linkuse as main transcript	c.637C>G	p.Gln213Glu	missense_variant	9/16	ENST00000370357.5	NP_775764.2
PASD1	XM_011531102.3 linkuse as main transcript	c.637C>G	p.Gln213Glu	missense_variant	9/16		XP_011529404.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PASD1	ENST00000370357.5 linkuse as main transcript	c.637C>G	p.Gln213Glu	missense_variant	9/16	1	NM_173493.3	ENSP00000359382	P1	Q8IV76-1
PASD1	ENST00000464219.1 linkuse as main transcript	n.775C>G		non_coding_transcript_exon_variant	9/15	2

Frequencies

GnomAD3 genomes

AF:

0.197

AC:

21810

AN:

110911

Hom.:

2042

Cov.:

AF XY:

0.190

AC XY:

6304

AN XY:

33145

show subpopulations

Gnomad AFR

AF:

0.0409

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.230

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.0272

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.285

Gnomad MID

AF:

0.289

Gnomad NFE

AF:

0.276

Gnomad OTH

AF:

0.227

GnomAD3 exomes

AF:

0.230

AC:

41663

AN:

180824

Hom.:

3485

AF XY:

0.236

AC XY:

15735

AN XY:

66674

show subpopulations

Gnomad AFR exome

AF:

0.0354

Gnomad AMR exome

AF:

0.248

Gnomad ASJ exome

AF:

0.308

Gnomad EAS exome

AF:

0.0175

Gnomad SAS exome

AF:

0.186

Gnomad FIN exome

AF:

0.311

Gnomad NFE exome

AF:

0.280

Gnomad OTH exome

AF:

0.251

GnomAD4 exome

AF:

0.261

AC:

286135

AN:

1096278

Hom.:

26474

Cov.:

AF XY:

0.260

AC XY:

93937

AN XY:

361972

show subpopulations

Gnomad4 AFR exome

AF:

0.0342

Gnomad4 AMR exome

AF:

0.243

Gnomad4 ASJ exome

AF:

0.308

Gnomad4 EAS exome

AF:

0.0352

Gnomad4 SAS exome

AF:

0.186

Gnomad4 FIN exome

AF:

0.314

Gnomad4 NFE exome

AF:

0.279

Gnomad4 OTH exome

AF:

0.244

GnomAD4 genome

AF:

0.196

AC:

21798

AN:

110966

Hom.:

2041

Cov.:

AF XY:

0.190

AC XY:

6303

AN XY:

33210

show subpopulations

Gnomad4 AFR

AF:

0.0408

Gnomad4 AMR

AF:

0.230

Gnomad4 ASJ

AF:

0.308

Gnomad4 EAS

AF:

0.0276

Gnomad4 SAS

AF:

0.185

Gnomad4 FIN

AF:

0.285

Gnomad4 NFE

AF:

0.276

Gnomad4 OTH

AF:

0.224

Alfa

AF:

0.243

Hom.:

2198

Bravo

AF:

0.187

TwinsUK

AF:

0.280

AC:

1040

ALSPAC

AF:

0.286

AC:

827

ESP6500AA

AF:

0.0415

AC:

159

ESP6500EA

AF:

0.277

AC:

1861

ExAC

AF:

0.227

AC:

27534

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.081

BayesDel_addAF

Benign

-0.80

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.2

DANN

Benign

0.94

DEOGEN2

Benign

0.0014

FATHMM_MKL

Benign

0.012

LIST_S2

Benign

0.46

MetaRNN

Benign

0.0057

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.4

MutationTaster

Benign

1.0

PrimateAI

Benign

0.28

PROVEAN

Benign

-0.35

REVEL

Benign

0.070

Sift

Uncertain

0.0030

Sift4G

Uncertain

0.027

Polyphen

0.74

Vest4

0.049

MPC

0.12

ClinPred

0.0089

GERP RS

1.1

Varity_R

0.087

gMVP

0.13

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over