Genetic Variant PSRC1:c.*609C>T (chr1-109279544-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.*609C>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 152,288 control chromosomes in the GnomAD database, including 35,004 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 ( 34921 hom., cov: 32)

Exomes 𝑓: 0.81 ( 83 hom. )

Consequence

PSRC1
NM_001032291.3 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.902

Publications

318 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:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 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.*609C>T	downstream_gene	N/A	NP_001027462.1
PSRC1	NM_001363309.2		c.*609C>T	downstream_gene	N/A	NP_001350238.1
PSRC1	NM_001394005.1		c.*609C>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.*609C>T	downstream_gene	N/A	ENSP00000358925.2
PSRC1	ENST00000369907.7	TSL:1	c.*609C>T	downstream_gene	N/A	ENSP00000358923.3
PSRC1	ENST00000369904.7	TSL:1	c.*577C>T	downstream_gene	N/A	ENSP00000358920.3

Frequencies

GnomAD3 genomes

AF:

0.638

AC:

96922

AN:

151912

Hom.:

34921

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:

0.922

Gnomad SAS

AF:

0.746

Gnomad FIN

AF:

0.775

Gnomad MID

AF:

0.850

Gnomad NFE

AF:

0.772

Gnomad OTH

AF:

0.685

GnomAD4 exome

AF:

0.810

AC:

209

AN:

258

Hom.:

Cov.:

AF XY:

0.808

AC XY:

118

AN XY:

146

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)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.809

AC:

157

AN:

194

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.833

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

96942

AN:

152030

Hom.:

34921

Cov.:

AF XY:

0.641

AC XY:

47669

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.276

AC:

11448

AN:

41414

American (AMR)

AF:

0.737

AC:

11252

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.828

AC:

2867

AN:

3464

East Asian (EAS)

AF:

0.922

AC:

4782

AN:

5184

South Asian (SAS)

AF:

0.747

AC:

3599

AN:

4820

European-Finnish (FIN)

AF:

0.775

AC:

8203

AN:

10580

Middle Eastern (MID)

AF:

0.842

AC:

246

AN:

292

European-Non Finnish (NFE)

AF:

0.772

AC:

52491

AN:

67984

Other (OTH)

AF:

0.688

AC:

1454

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1404

2809

4213

5618

7022

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

768

1536

2304

3072

3840

<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:

0.731

Hom.:

159910

Bravo

AF:

0.618

Asia WGS

AF:

0.790

AC:

2749

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.0

(source)

DANN

Benign

0.81

PhyloP100

-0.90

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