NM_020714.3:c.162+1353A>G

Variant names:

• chr19-12607805-T-C
• rs4804202
• NM_020714.3:c.162+1353A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_020714.3(ZNF490):​c.162+1353A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 151,354 control chromosomes in the GnomAD database, including 27,248 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 0.59 (27248 hom., cov: 29)
• Consequence: ZNF490 NM_020714.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 8 publications found

Genes affected

ZNF490 (HGNC:23705): (zinc finger protein 490) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020714.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF490	NM_020714.3	MANE Select	c.162+1353A>G		intron	N/A	NP_065765.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF490	ENST00000311437.11	TSL:1 MANE Select	c.162+1353A>G		intron	N/A	ENSP00000311521.6
	ZNF490	ENST00000414906.5	TSL:3	n.*84+1353A>G		intron	N/A	ENSP00000402719.1
	ZNF490	ENST00000465656.1	TSL:4	n.461+1353A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.587 AC: 88781 AN: 151258 Hom.: 27218 Cov.: 29

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.587 AC: 88854 AN: 151354 Hom.: 27248 Cov.: 29 AF XY: 0.576 AC XY: 42522 AN XY: 73862

African (AFR) AF: 0.482 AC: 19876 AN: 41200

American (AMR) AF: 0.534 AC: 8108 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2574 AN: 3466

East Asian (EAS) AF: 0.181 AC: 929 AN: 5124

South Asian (SAS) AF: 0.424 AC: 2032 AN: 4788

European-Finnish (FIN) AF: 0.620 AC: 6439 AN: 10382

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.689 AC: 46810 AN: 67908

Other (OTH) AF: 0.616 AC: 1292 AN: 2098

Alfa AF: 0.656 Hom.: 50941

Bravo AF: 0.576

Asia WGS AF: 0.339 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	8.6
DANN	Benign	0.88
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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: rs4804202; hg19: chr19-12718619;