dbSNP rs6006486: PARVB:c.273+7630C>A (chr22-44107753-C-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_013327.5(PARVB):c.273+7630C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,074 control chromosomes in the GnomAD database, including 5,606 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 ( 5605 hom., cov: 32)

Exomes 𝑓: 0.30 ( 1 hom. )

Consequence

PARVB
NM_013327.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.40

Publications

2 publications found

Variant links:

Genes affected

PARVB (HGNC:14653): (parvin beta) This gene encodes a member of the parvin family of actin-binding proteins, which play a role in cytoskeleton organization and cell adhesion. These proteins are associated with focal contacts and contain calponin homology domains that bind to actin filaments. This family member binds to alphaPIX and alpha-actinin, and it can inhibit the activity of integrin-linked kinase. This protein also functions in tumor suppression. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]

PARVB links:

ENSG00000279175 (HGNC:):

ENSG00000279175 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=-1.03).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013327.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PARVB	NM_013327.5	MANE Select	c.273+7630C>A	intron	N/A	NP_037459.2
PARVB	NM_001003828.3		c.372+7630C>A	intron	N/A	NP_001003828.1
PARVB	NM_001243385.2		c.162+7630C>A	intron	N/A	NP_001230314.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PARVB	ENST00000338758.12	TSL:1 MANE Select	c.273+7630C>A	intron	N/A	ENSP00000342492.6
PARVB	ENST00000406477.7	TSL:1	c.372+7630C>A	intron	N/A	ENSP00000384515.3
PARVB	ENST00000404989.1	TSL:1	c.162+7630C>A	intron	N/A	ENSP00000384353.1

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40251

AN:

151926

Hom.:

5593

Cov.:

show subpopulations

Gnomad AFR

AF:

0.221

Gnomad AMI

AF:

0.300

Gnomad AMR

AF:

0.305

Gnomad ASJ

AF:

0.373

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.298

GnomAD4 exome

AF:

0.300

AC:

AN:

Hom.:

Cov.:

AF XY:

0.318

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.321

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.546

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.265

AC:

40292

AN:

152044

Hom.:

5605

Cov.:

AF XY:

0.259

AC XY:

19238

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.221

AC:

9157

AN:

41478

American (AMR)

AF:

0.305

AC:

4659

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.373

AC:

1296

AN:

3470

East Asian (EAS)

AF:

0.209

AC:

1076

AN:

5158

South Asian (SAS)

AF:

0.231

AC:

1114

AN:

4820

European-Finnish (FIN)

AF:

0.192

AC:

2027

AN:

10578

Middle Eastern (MID)

AF:

0.398

AC:

117

AN:

294

European-Non Finnish (NFE)

AF:

0.293

AC:

19931

AN:

67950

Other (OTH)

AF:

0.305

AC:

641

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1527

3054

4582

6109

7636

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

422

844

1266

1688

2110

<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:

0.289

Hom.:

28839

Bravo

AF:

0.273

Asia WGS

AF:

0.256

AC:

889

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

0.12

(source)

DANN

Benign

0.42

PhyloP100

-2.4

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over