rs321930

Variant names:

• chr19-52331957-A-G
• rs321930
• XM_047438286.1:c.-399A>G

Variant summary

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

The XM_047438286.1(ZNF610):​c.-399A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,206 control chromosomes in the GnomAD database, including 4,972 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 0.23 (4972 hom., cov: 32)
• Consequence: ZNF610 XM_047438286.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

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]

ENSG00000269535 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF610	XM_047438286.1	c.-399A>G		5_prime_UTR_variant	Exon 1 of 6		XP_047294242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000269535	ENST00000594379.1	n.200-1567T>C		intron_variant	Intron 1 of 6	2

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34760 AN: 152088 Hom.: 4947 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0217

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.229 AC: 34823 AN: 152206 Hom.: 4972 Cov.: 32 AF XY: 0.221 AC XY: 16450 AN XY: 74408

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.0961

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.223

Alfa AF: 0.191 Hom.: 4133

Bravo AF: 0.239

Asia WGS AF: 0.0950 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.8
DANN	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs321930; hg19: chr19-52835210;