rs10407762

Positions:

• chr19-52784848-C-T

Variant summary

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

The NM_001321866.4(ZNF600):​c.-643+1747G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,200 control chromosomes in the GnomAD database, including 1,648 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 0.14 (1648 hom., cov: 32)
• Consequence: ZNF600 NM_001321866.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

ZNF600 (HGNC:30951): (zinc finger protein 600) Predicted to enable DNA-binding transcription activator 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF600	NM_001321866.4	c.-643+1747G>A		intron_variant		ENST00000692063.1	NP_001308795.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF600	ENST00000692063.1	c.-643+1747G>A		intron_variant			NM_001321866.4	ENSP00000509267	P1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21627 AN: 152082 Hom.: 1646 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0633

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.142 AC: 21648 AN: 152200 Hom.: 1648 Cov.: 32 AF XY: 0.139 AC XY: 10318 AN XY: 74426

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0632

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.160

Alfa AF: 0.158 Hom.: 2891

Bravo AF: 0.147

Asia WGS AF: 0.0390 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.25

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: rs10407762; hg19: chr19-53288101;