rs2092351

Variant names:

• chr22-44178524-G-A
• rs2092351
• ENST00000453888.7:n.209-4794G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-44178524-G-A
• chr22-44178524-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000453888.7(PARVG):​n.209-4794G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PARVG	NM_001137605.3	c.-188-3218G>A		intron_variant	Intron 1 of 13		NP_001131077.1
PARVG	XM_047441455.1	c.190-4794G>A		intron_variant	Intron 1 of 10		XP_047297411.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARVG	ENST00000453888.7	n.209-4794G>A		intron_variant	Intron 1 of 3	1
PARVG	ENST00000422871.5	c.-188-3218G>A		intron_variant	Intron 1 of 13	5		ENSP00000391453.1

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

African (AFR) AF: 0.413 AC: 17114 AN: 41442

American (AMR) AF: 0.397 AC: 6070 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1258 AN: 3472

East Asian (EAS) AF: 0.704 AC: 3648 AN: 5184

South Asian (SAS) AF: 0.363 AC: 1748 AN: 4816

European-Finnish (FIN) AF: 0.410 AC: 4316 AN: 10520

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25192 AN: 67968

Other (OTH) AF: 0.387 AC: 819 AN: 2114

Alfa AF: 0.378 Hom.: 35693

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
PhyloP100		-0.097
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: rs2092351; hg19: chr22-44574404;