19-55579966-G-C

Position:

• chr19-55579966-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_152600.3(ZNF579):​c.-2-325C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00902 in 288,536 control chromosomes in the GnomAD database, including 21 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 0.0085 (10 hom., cov: 32)
  • Exomes 𝑓: 0.0096 (11 hom.)
• Consequence: ZNF579 NM_152600.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

Genes affected

ZNF579 (HGNC:26646): (zinc finger protein 579) Enables RNA binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS2: High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF579	NM_152600.3	c.-2-325C>G		intron_variant		ENST00000325421.7	NP_689813.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF579	ENST00000325421.7	c.-2-325C>G		intron_variant		2	NM_152600.3	ENSP00000320188	P1
ZNF579	ENST00000592239.1	c.-327C>G		5_prime_UTR_variant	2/2	4		ENSP00000465146

Frequencies

GnomAD3 genomes AF: 0.00851 AC: 1295 AN: 152106 Hom.: 10 Cov.: 32

Gnomad AFR AF: 0.00249

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0103

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0142

Gnomad OTH AF: 0.0206

GnomAD4 exome AF: 0.00960 AC: 1309 AN: 136312 Hom.: 11 Cov.: 0 AF XY: 0.00947 AC XY: 655 AN XY: 69156

Gnomad4 AFR exome AF: 0.00190

Gnomad4 AMR exome AF: 0.0145

Gnomad4 ASJ exome AF: 0.00442

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00123

Gnomad4 NFE exome AF: 0.0129

Gnomad4 OTH exome AF: 0.00923

GnomAD4 genome AF: 0.00851 AC: 1295 AN: 152224 Hom.: 10 Cov.: 32 AF XY: 0.00743 AC XY: 553 AN XY: 74428

Gnomad4 AFR AF: 0.00248

Gnomad4 AMR AF: 0.0103

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.0142

Gnomad4 OTH AF: 0.0204

Alfa AF: 0.00948 Hom.: 1

Bravo AF: 0.00918

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.58

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: rs149546760; hg19: chr19-56091332;