NM_018222.5:c.137-25895A>G

Variant names:

• chr11-12447850-A-G
• rs7120489
• NM_018222.5:c.137-25895A>G

Variant summary

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

The NM_018222.5(PARVA):​c.137-25895A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 152,236 control chromosomes in the GnomAD database, including 58,011 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 0.86 (58011 hom., cov: 32)
• Consequence: PARVA NM_018222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 11 publications found

Genes affected

PARVA (HGNC:14652): (parvin alpha) This gene encodes a member of the parvin family of actin-binding proteins. Parvins are associated with focal contacts and contain calponin homology domains that bind to actin filaments. The encoded protein is part of the integrin-linked kinase signaling complex and plays a role in cell adhesion, motility and survival. [provided by RefSeq, Dec 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018222.5. 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
	PARVA	NM_018222.5	MANE Select	c.137-25895A>G		intron	N/A	NP_060692.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARVA	ENST00000334956.15	TSL:1 MANE Select	c.137-25895A>G		intron	N/A	ENSP00000334008.9
	PARVA	ENST00000530755.5	TSL:2	n.222-25895A>G		intron	N/A
	PARVA	ENST00000533345.5	TSL:5	n.114-25895A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.862 AC: 131176 AN: 152118 Hom.: 57980 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.862 AC: 131252 AN: 152236 Hom.: 58011 Cov.: 32 AF XY: 0.869 AC XY: 64647 AN XY: 74430

African (AFR) AF: 0.643 AC: 26683 AN: 41494

American (AMR) AF: 0.938 AC: 14350 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3229 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5181 AN: 5182

South Asian (SAS) AF: 0.960 AC: 4628 AN: 4822

European-Finnish (FIN) AF: 0.981 AC: 10422 AN: 10620

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63708 AN: 68026

Other (OTH) AF: 0.896 AC: 1892 AN: 2112

Alfa AF: 0.908 Hom.: 120630

Bravo AF: 0.847

Asia WGS AF: 0.954 AC: 3317 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	0.089
DANN	Benign	0.33
PhyloP100		-2.2
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: rs7120489; hg19: chr11-12469397;