rs2657940

chr19-52360583-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001161425.2(ZNF610):c.320-5115G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,122 control chromosomes in the GnomAD database, including 2,873 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 0.18 (2873 hom., cov: 32)
• Consequence: ZNF610 NM_001161425.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF610	NM_001161425.2	c.320-5115G>A		intron_variant		ENST00000403906.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF610	ENST00000403906.8	c.320-5115G>A		intron_variant		1	NM_001161425.2	P1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27697 AN: 152004 Hom.: 2867 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.182 AC: 27712 AN: 152122 Hom.: 2873 Cov.: 32 AF XY: 0.181 AC XY: 13452 AN XY: 74350

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.179

Alfa AF: 0.214 Hom.: 7429

Bravo AF: 0.178

Asia WGS AF: 0.229 AC: 795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	13
Dann	Benign	0.95

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: rs2657940; hg19: chr19-52863836;