19-52360714-A-G

Variant names:

• chr19-52360714-A-G
• rs2263901
• NM_001161425.2:c.320-4984A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001161425.2(ZNF610):​c.320-4984A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,122 control chromosomes in the GnomAD database, including 3,165 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 0.20 (3165 hom., cov: 32)
• Consequence: ZNF610 NM_001161425.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09
• Publications: 2 publications found

Genes affected

ZNF610 (HGNC:26687): (zinc finger protein 610) 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001161425.2. 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
	ZNF610	NM_001161425.2	MANE Select	c.320-4984A>G		intron	N/A	NP_001154897.1	Q8N9Z0-1
	ZNF610	NM_001161426.2		c.320-4984A>G		intron	N/A	NP_001154898.1	Q8N9Z0-1
	ZNF610	NM_173530.3		c.320-4984A>G		intron	N/A	NP_775801.2	Q8N9Z0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF610	ENST00000403906.8	TSL:1 MANE Select	c.320-4984A>G		intron	N/A	ENSP00000383922.2	Q8N9Z0-1
	ZNF610	ENST00000321287.12	TSL:1	c.320-4984A>G		intron	N/A	ENSP00000324441.8	Q8N9Z0-1
	ZNF610	ENST00000601151.5	TSL:1	c.191-4984A>G		intron	N/A	ENSP00000471021.1	Q8N9Z0-2

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30123 AN: 152004 Hom.: 3159 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.198 AC: 30155 AN: 152122 Hom.: 3165 Cov.: 32 AF XY: 0.196 AC XY: 14552 AN XY: 74368

African (AFR) AF: 0.154 AC: 6373 AN: 41480

American (AMR) AF: 0.171 AC: 2614 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3466

East Asian (EAS) AF: 0.323 AC: 1674 AN: 5176

South Asian (SAS) AF: 0.162 AC: 782 AN: 4822

European-Finnish (FIN) AF: 0.196 AC: 2076 AN: 10590

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15280 AN: 67982

Other (OTH) AF: 0.191 AC: 404 AN: 2110

Alfa AF: 0.207 Hom.: 1489

Bravo AF: 0.196

Asia WGS AF: 0.236 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.58
DANN	Benign	0.34
PhyloP100		-3.1
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: rs2263901; hg19: chr19-52863967;