chr22-44173534-C-T

Variant names:

• chr22-44173534-C-T
• rs7292425
• ENST00000453888.7:n.208+343C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000453888.7(PARVG):​n.208+343C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000361 in 138,472 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000036 (0 hom., cov: 32)
• Consequence: PARVG ENST00000453888.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558
• Publications: 6 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARVG	NM_001137605.3	c.-189+343C>T		intron_variant	Intron 1 of 13		NP_001131077.1
PARVG	XM_047441455.1	c.189+343C>T		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.208+343C>T		intron_variant	Intron 1 of 3	1
PARVG	ENST00000422871.5	c.-189+343C>T		intron_variant	Intron 1 of 13	5		ENSP00000391453.1

Frequencies

GnomAD3 genomes AF: 0.0000361 AC: 5 AN: 138472 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000291

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000695

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000158

Gnomad OTH AF: 0.000522

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

GnomAD4 genome AF: 0.0000361 AC: 5 AN: 138472 Hom.: 0 Cov.: 32 AF XY: 0.0000590 AC XY: 4 AN XY: 67832

African (AFR) AF: 0.0000291 AC: 1 AN: 34348

American (AMR) AF: 0.0000695 AC: 1 AN: 14388

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3322

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5154

South Asian (SAS) AF: 0.00 AC: 0 AN: 4730

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10050

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0000158 AC: 1 AN: 63438

Other (OTH) AF: 0.000522 AC: 1 AN: 1916

Alfa AF: 0.00 Hom.: 3471

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.62
DANN	Benign	0.63
PhyloP100		-0.56

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: rs7292425; hg19: chr22-44569414;