rs10831841

chr11-12524745-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018222.5(PARVA):c.1043-3104G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,926 control chromosomes in the GnomAD database, including 7,685 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 0.32 (7685 hom., cov: 34)
• Consequence: PARVA NM_018222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARVA	NM_018222.5	c.1043-3104G>A		intron_variant		ENST00000334956.15
PARVA	XM_005253015.4	c.911-3104G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARVA	ENST00000334956.15	c.1043-3104G>A		intron_variant		1	NM_018222.5	P1

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48049 AN: 151808 Hom.: 7677 Cov.: 34

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.316 AC: 48084 AN: 151926 Hom.: 7685 Cov.: 34 AF XY: 0.317 AC XY: 23565 AN XY: 74276

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.352

Alfa AF: 0.341 Hom.: 10592

Bravo AF: 0.316

Asia WGS AF: 0.353 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.4
Dann	Benign	0.42

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

LitVar

Other links and lift over

dbSNP: rs10831841; hg19: chr11-12546292;