16-71476073-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_006961.4(ZNF19):c.474G>A(p.Arg158=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00554 in 1,614,166 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0037 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0057 (35 hom.)
• Consequence: ZNF19 NM_006961.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.788

Genes affected

ZNF19 (HGNC:12981): (zinc finger protein 19) The protein encoded by this gene contains a zinc finger, a nucleic acid-binding domain present in many transcription factors. This gene is located in a region next to ZNF23, a gene also encoding a zinc finger protein, on chromosome 16. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BP6: Variant 16-71476073-C-T is Benign according to our data. Variant chr16-71476073-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2646799.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.788 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF19	NM_006961.4	c.474G>A	p.Arg158=	synonymous_variant	6/6	ENST00000288177.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF19	ENST00000288177.10	c.474G>A	p.Arg158=	synonymous_variant	6/6	1	NM_006961.4	P1

Frequencies

GnomAD3 genomes AF: 0.00368 AC: 560 AN: 152210 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00147

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.00314

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000848

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00606

Gnomad OTH AF: 0.000957

GnomAD3 exomes AF: 0.00290 AC: 729 AN: 251310 Hom.: 3 AF XY: 0.00279 AC XY: 379 AN XY: 135826

Gnomad AFR exome AF: 0.00105

Gnomad AMR exome AF: 0.00179

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000832

Gnomad NFE exome AF: 0.00539

Gnomad OTH exome AF: 0.00310

GnomAD4 exome AF: 0.00574 AC: 8389 AN: 1461838 Hom.: 35 Cov.: 34 AF XY: 0.00554 AC XY: 4026 AN XY: 727220

Gnomad4 AFR exome AF: 0.000926

Gnomad4 AMR exome AF: 0.00192

Gnomad4 ASJ exome AF: 0.0000765

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000209

Gnomad4 FIN exome AF: 0.00109

Gnomad4 NFE exome AF: 0.00716

Gnomad4 OTH exome AF: 0.00378

GnomAD4 genome AF: 0.00368 AC: 560 AN: 152328 Hom.: 1 Cov.: 32 AF XY: 0.00322 AC XY: 240 AN XY: 74498

Gnomad4 AFR AF: 0.00147

Gnomad4 AMR AF: 0.00313

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000848

Gnomad4 NFE AF: 0.00606

Gnomad4 OTH AF: 0.000947

Alfa AF: 0.00463 Hom.: 1

Bravo AF: 0.00399

Asia WGS AF: 0.000866 AC: 3 AN: 3478

EpiCase AF: 0.00480

EpiControl AF: 0.00510

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2022

ZNF19: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
Cadd	Benign	7.4
Dann	Benign	0.78

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: rs147578256; hg19: chr16-71509976; COSMIC: COSV55507824; COSMIC: COSV55507824;