rs4804202

Positions:

• chr19-12607805-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF490	NM_020714.3	c.162+1353A>G		intron_variant		ENST00000311437.11	NP_065765.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF490	ENST00000311437.11	c.162+1353A>G		intron_variant		1	NM_020714.3	ENSP00000311521	P1
ZNF490	ENST00000414906.5	c.*84+1353A>G		intron_variant, NMD_transcript_variant		3		ENSP00000402719
ZNF490	ENST00000465656.1	n.461+1353A>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.616

Alfa AF: 0.662 Hom.: 40877

Bravo AF: 0.576

Asia WGS AF: 0.339 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	8.6
DANN	Benign	0.88

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: rs4804202; hg19: chr19-12718619;