rs2092351

chr22-44178524-G-Achr22-44178524-G-C

Variant summary

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

The ENST00000453888.7(PARVG):n.209-4794G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,996 control chromosomes in the GnomAD database, including 12,403 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 0.40 (12403 hom., cov: 33)
• Consequence: PARVG ENST00000453888.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARVG	NM_001137605.3	c.-188-3218G>A		intron_variant
PARVG	XM_047441455.1	c.190-4794G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARVG	ENST00000453888.7	n.209-4794G>A		intron_variant, non_coding_transcript_variant		1
PARVG	ENST00000422871.5	c.-188-3218G>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60651 AN: 151876 Hom.: 12390 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.399 AC: 60695 AN: 151996 Hom.: 12403 Cov.: 33 AF XY: 0.402 AC XY: 29867 AN XY: 74282

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.387

Alfa AF: 0.375 Hom.: 22492

Bravo AF: 0.400

Asia WGS AF: 0.498 AC: 1732 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.8
Dann	Benign	0.65

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: rs2092351; hg19: chr22-44574404;