rs10219167

Positions:

• chr11-12382289-G-A
• chr11-12382289-G-T

Variant summary

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

The NM_018222.5(PARVA):​c.136+4506G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 151,896 control chromosomes in the GnomAD database, including 38,381 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 0.66 (38381 hom., cov: 32)
• Consequence: PARVA NM_018222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARVA	NM_018222.5	c.136+4506G>A		intron_variant		ENST00000334956.15
PARVA	XM_005253015.4	c.4+5555G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARVA	ENST00000334956.15	c.136+4506G>A		intron_variant		1	NM_018222.5	P1
PARVA	ENST00000530755.5	n.221+4506G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100235 AN: 151780 Hom.: 38364 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.660 AC: 100260 AN: 151896 Hom.: 38381 Cov.: 32 AF XY: 0.665 AC XY: 49389 AN XY: 74252

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.682

Alfa AF: 0.803 Hom.: 46266

Bravo AF: 0.632

Asia WGS AF: 0.802 AC: 2786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.74

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: rs10219167; hg19: chr11-12403836;