rs139161

Variant names:

• chr22-44201716-G-A
• rs139161
• NM_022141.7:c.813+2994G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022141.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARVG	NM_022141.7	MANE Select	c.813+2994G>A		intron	N/A	NP_071424.1
	PARVG	NM_001137605.3		c.813+2994G>A		intron	N/A	NP_001131077.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARVG	ENST00000444313.8	TSL:1 MANE Select	c.813+2994G>A		intron	N/A	ENSP00000391583.2
	PARVG	ENST00000422871.5	TSL:5	c.813+2994G>A		intron	N/A	ENSP00000391453.1
	PARVG	ENST00000356909.7	TSL:5	n.*249+2994G>A		intron	N/A	ENSP00000349378.3

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

African (AFR) AF: 0.133 AC: 5509 AN: 41524

American (AMR) AF: 0.231 AC: 3530 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3468

East Asian (EAS) AF: 0.104 AC: 539 AN: 5174

South Asian (SAS) AF: 0.140 AC: 676 AN: 4830

European-Finnish (FIN) AF: 0.310 AC: 3278 AN: 10580

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14580 AN: 68004

Other (OTH) AF: 0.184 AC: 390 AN: 2114

Alfa AF: 0.208 Hom.: 441

Bravo AF: 0.187

Asia WGS AF: 0.117 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.54
PhyloP100		-0.36
Mutation Taster		=99/1	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: rs139161; hg19: chr22-44597596;