rs10831841

Variant names:

• chr11-12524745-G-A
• rs10831841
• NM_018222.5:c.1043-3104G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.393 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.1043-3104G>A		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.1043-3104G>A		intron	N/A	ENSP00000334008.9

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

African (AFR) AF: 0.257 AC: 10639 AN: 41476

American (AMR) AF: 0.341 AC: 5214 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1383 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1711 AN: 5174

South Asian (SAS) AF: 0.408 AC: 1961 AN: 4810

European-Finnish (FIN) AF: 0.275 AC: 2908 AN: 10556

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23223 AN: 67842

Other (OTH) AF: 0.352 AC: 742 AN: 2108

Alfa AF: 0.337 Hom.: 14295

Bravo AF: 0.316

Asia WGS AF: 0.353 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.42
PhyloP100		0.57
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: rs10831841; hg19: chr11-12546292;