rs10219167

Variant names:

• chr11-12382289-G-A
• rs10219167
• NM_018222.5:c.136+4506G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

ENSG00000303854 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PARVA	NM_018222.5	c.136+4506G>A		intron_variant	Intron 1 of 12	ENST00000334956.15	NP_060692.3
PARVA	XM_005253015.4	c.4+5555G>A		intron_variant	Intron 1 of 12		XP_005253072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARVA	ENST00000334956.15	c.136+4506G>A		intron_variant	Intron 1 of 12	1	NM_018222.5	ENSP00000334008.9
PARVA	ENST00000530755.5	n.221+4506G>A		intron_variant	Intron 1 of 3	2
ENSG00000303854	ENST00000797536.1	n.68-820C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.241 AC: 9958 AN: 41304

American (AMR) AF: 0.730 AC: 11143 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2654 AN: 3464

East Asian (EAS) AF: 0.900 AC: 4664 AN: 5182

South Asian (SAS) AF: 0.812 AC: 3911 AN: 4816

European-Finnish (FIN) AF: 0.853 AC: 9012 AN: 10570

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56548 AN: 67980

Other (OTH) AF: 0.682 AC: 1436 AN: 2106

Alfa AF: 0.784 Hom.: 56517

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
PhyloP100		-1.0
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: rs10219167; hg19: chr11-12403836;