dbSNP rs1277930: PSRC1:c.*632C>T (chr1-109279521-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_001032291.3(PSRC1):c.*632C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,134 control chromosomes in the GnomAD database, including 35,003 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 0.64 ( 34952 hom., cov: 33)

Exomes 𝑓: 0.83 ( 51 hom. )

Consequence

PSRC1
NM_001032291.3 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.17

Publications

40 publications found

Variant links:

Genes affected

PSRC1 (HGNC:24472): (proline and serine rich coiled-coil 1) This gene encodes a proline-rich protein that is a target for regulation by the tumor suppressor protein p53. The encoded protein plays an important role in mitosis by recruiting and regulating microtubule depolymerases that destabalize microtubules. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Apr 2014]

PSRC1 links:

Genome browser will be placed here

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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001032291.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PSRC1	NM_001032291.3	MANE Select	c.*632C>T	downstream_gene	N/A	NP_001027462.1
PSRC1	NM_001363309.2		c.*632C>T	downstream_gene	N/A	NP_001350238.1
PSRC1	NM_001394005.1		c.*632C>T	downstream_gene	N/A	NP_001380934.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PSRC1	ENST00000369909.7	TSL:1 MANE Select	c.*632C>T	downstream_gene	N/A	ENSP00000358925.2
PSRC1	ENST00000369907.7	TSL:1	c.*632C>T	downstream_gene	N/A	ENSP00000358923.3
PSRC1	ENST00000369904.7	TSL:1	c.*600C>T	downstream_gene	N/A	ENSP00000358920.3

Frequencies

GnomAD3 genomes

AF:

0.638

AC:

96929

AN:

151864

Hom.:

34950

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.658

Gnomad AMR

AF:

0.737

Gnomad ASJ

AF:

0.828

Gnomad EAS

AF:

0.932

Gnomad SAS

AF:

0.748

Gnomad FIN

AF:

0.775

Gnomad MID

AF:

0.854

Gnomad NFE

AF:

0.772

Gnomad OTH

AF:

0.686

GnomAD4 exome

AF:

0.829

AC:

126

AN:

152

Hom.:

Cov.:

AF XY:

0.845

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.828

AC:

AN:

116

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.875

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.638

AC:

96951

AN:

151982

Hom.:

34952

Cov.:

AF XY:

0.642

AC XY:

47674

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.276

AC:

11458

AN:

41448

American (AMR)

AF:

0.737

AC:

11255

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.828

AC:

2871

AN:

3468

East Asian (EAS)

AF:

0.933

AC:

4837

AN:

5186

South Asian (SAS)

AF:

0.748

AC:

3607

AN:

4822

European-Finnish (FIN)

AF:

0.775

AC:

8174

AN:

10544

Middle Eastern (MID)

AF:

0.846

AC:

247

AN:

292

European-Non Finnish (NFE)

AF:

0.772

AC:

52450

AN:

67938

Other (OTH)

AF:

0.689

AC:

1453

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1435

2870

4305

5740

7175

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

766

1532

2298

3064

3830

<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:

0.719

Hom.:

53693

Bravo

AF:

0.619

Asia WGS

AF:

0.810

AC:

2818

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.67

(source)

DANN

Benign

0.25

PhyloP100

-1.2

Splicing

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