rs12935091

Variant names:

• chr16-71491305-A-G
• rs12935091
• ENST00000564225.5:c.-190+3649T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000564225.5(ZNF19):​c.-190+3649T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0297 in 152,294 control chromosomes in the GnomAD database, including 91 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 0.030 (91 hom., cov: 32)
• Consequence: ZNF19 ENST00000564225.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0297 (4529/152294) while in subpopulation NFE AF = 0.0474 (3223/68016). AF 95% confidence interval is 0.046. There are 91 homozygotes in GnomAd4. There are 2104 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 91 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF19	ENST00000564225.5	c.-190+3649T>C		intron_variant	Intron 2 of 5	2		ENSP00000455575.1
ZNF19	ENST00000566202.5	c.-189-6557T>C		intron_variant	Intron 2 of 4	5		ENSP00000454862.1
ZNF19	ENST00000568446.1	n.324+3649T>C		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0298 AC: 4530 AN: 152176 Hom.: 91 Cov.: 32

Gnomad AFR AF: 0.00849

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0207

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00850

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0474

Gnomad OTH AF: 0.0267

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

GnomAD4 genome AF: 0.0297 AC: 4529 AN: 152294 Hom.: 91 Cov.: 32 AF XY: 0.0283 AC XY: 2104 AN XY: 74458

African (AFR) AF: 0.00847 AC: 352 AN: 41580

American (AMR) AF: 0.0207 AC: 316 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.00851 AC: 41 AN: 4818

European-Finnish (FIN) AF: 0.0444 AC: 471 AN: 10610

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0474 AC: 3223 AN: 68016

Other (OTH) AF: 0.0269 AC: 57 AN: 2116

Alfa AF: 0.0384 Hom.: 89

Bravo AF: 0.0268

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.58
PhyloP100		-0.017

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12935091; hg19: chr16-71525208;