rs2657940

Variant names:

• chr19-52360583-G-A
• rs2657940
• NM_001161425.2:c.320-5115G>A

Variant summary

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

The NM_001161425.2(ZNF610):​c.320-5115G>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
• Publications: 6 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=-0.69).
• 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 rank	MANE	Protein	UniProt
ZNF610	NM_001161425.2	c.320-5115G>A		intron_variant	Intron 5 of 5	ENST00000403906.8	NP_001154897.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF610	ENST00000403906.8	c.320-5115G>A		intron_variant	Intron 5 of 5	1	NM_001161425.2	ENSP00000383922.2

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

African (AFR) AF: 0.102 AC: 4253 AN: 41524

American (AMR) AF: 0.166 AC: 2531 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3470

East Asian (EAS) AF: 0.323 AC: 1665 AN: 5154

South Asian (SAS) AF: 0.162 AC: 778 AN: 4804

European-Finnish (FIN) AF: 0.197 AC: 2087 AN: 10578

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15228 AN: 67988

Other (OTH) AF: 0.179 AC: 378 AN: 2110

Alfa AF: 0.209 Hom.: 14989

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
PhyloP100		0.14
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: rs2657940; hg19: chr19-52863836;