19-55579966-G-C

Variant names:

• chr19-55579966-G-C
• rs149546760
• NM_152600.3:c.-2-325C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152600.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF579	NM_152600.3	MANE Select	c.-2-325C>G		intron	N/A	NP_689813.2	Q8NAF0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF579	ENST00000325421.7	TSL:2 MANE Select	c.-2-325C>G		intron	N/A	ENSP00000320188.3	Q8NAF0
	ZNF579	ENST00000856087.1		c.-327C>G		5_prime_UTR	Exon 2 of 2	ENSP00000526146.1
	ZNF579	ENST00000592239.1	TSL:4	c.-327C>G		5_prime_UTR	Exon 2 of 2	ENSP00000465146.1	K7EJF4

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

African (AFR) AF: 0.00190 AC: 8 AN: 4210

American (AMR) AF: 0.0145 AC: 54 AN: 3736

Ashkenazi Jewish (ASJ) AF: 0.00442 AC: 23 AN: 5198

East Asian (EAS) AF: 0.00 AC: 0 AN: 12204

South Asian (SAS) AF: 0.00 AC: 0 AN: 2244

European-Finnish (FIN) AF: 0.00123 AC: 14 AN: 11400

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 756

European-Non Finnish (NFE) AF: 0.0129 AC: 1125 AN: 87350

Other (OTH) AF: 0.00923 AC: 85 AN: 9214

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

African (AFR) AF: 0.00248 AC: 103 AN: 41526

American (AMR) AF: 0.0103 AC: 157 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00 AC: 0 AN: 4814

European-Finnish (FIN) AF: 0.000377 AC: 4 AN: 10620

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0142 AC: 967 AN: 68010

Other (OTH) AF: 0.0204 AC: 43 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		-0.27
Mutation Taster		=100/0	polymorphism

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: rs149546760; hg19: chr19-56091332;