22-44058858-G-A

Variant names:

• chr22-44058858-G-A
• rs5764495
• NM_013327.5:c.112+34407G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013327.5(PARVB):​c.112+34407G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,574 control chromosomes in the GnomAD database, including 30,778 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 0.62 (30778 hom., cov: 29)
• Consequence: PARVB NM_013327.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.64
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• 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_013327.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARVB	NM_013327.5	MANE Select	c.112+34407G>A		intron	N/A	NP_037459.2
	PARVB	NM_001003828.3		c.212-35070G>A		intron	N/A	NP_001003828.1
	PARVB	NM_001243386.2		c.-45+32482G>A		intron	N/A	NP_001230315.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARVB	ENST00000338758.12	TSL:1 MANE Select	c.112+34407G>A		intron	N/A	ENSP00000342492.6
	PARVB	ENST00000406477.7	TSL:1	c.212-35070G>A		intron	N/A	ENSP00000384515.3
	PARVB	ENST00000619710.4	TSL:1	c.-45+32482G>A		intron	N/A	ENSP00000482511.1

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93652 AN: 151456 Hom.: 30736 Cov.: 29

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.575

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.618 AC: 93746 AN: 151574 Hom.: 30778 Cov.: 29 AF XY: 0.625 AC XY: 46258 AN XY: 74062

African (AFR) AF: 0.813 AC: 33665 AN: 41392

American (AMR) AF: 0.552 AC: 8396 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2031 AN: 3466

East Asian (EAS) AF: 0.923 AC: 4723 AN: 5116

South Asian (SAS) AF: 0.721 AC: 3456 AN: 4794

European-Finnish (FIN) AF: 0.565 AC: 5940 AN: 10510

Middle Eastern (MID) AF: 0.524 AC: 150 AN: 286

European-Non Finnish (NFE) AF: 0.497 AC: 33671 AN: 67788

Other (OTH) AF: 0.573 AC: 1206 AN: 2104

Alfa AF: 0.529 Hom.: 36955

Bravo AF: 0.624

Asia WGS AF: 0.779 AC: 2710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.41
PhyloP100		-3.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5764495; hg19: chr22-44454738; COSMIC: COSV58691334;