rs139161

chr22-44201716-G-A

Variant summary

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

The NM_022141.7(PARVG):c.813+2994G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,196 control chromosomes in the GnomAD database, including 3,065 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 0.19 (3065 hom., cov: 34)
• Consequence: PARVG NM_022141.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

Genes affected

PARVG (HGNC:14654): (parvin gamma) Members of the parvin family, including PARVG, are actin-binding proteins associated with focal contacts.[supplied by OMIM, Aug 2004]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARVG	NM_022141.7	c.813+2994G>A		intron_variant		ENST00000444313.8
PARVG	NM_001137605.3	c.813+2994G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARVG	ENST00000444313.8	c.813+2994G>A		intron_variant		1	NM_022141.7	P1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29440 AN: 152076 Hom.: 3065 Cov.: 34

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.194 AC: 29451 AN: 152196 Hom.: 3065 Cov.: 34 AF XY: 0.197 AC XY: 14677 AN XY: 74394

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.184

Alfa AF: 0.210 Hom.: 428

Bravo AF: 0.187

Asia WGS AF: 0.117 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.3
Dann	Benign	0.54

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: rs139161; hg19: chr22-44597596;