rs10407762

Variant names:

• chr19-52784848-C-T
• rs10407762
• NM_001321866.4:c.-643+1747G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF600	NM_001321866.4	c.-643+1747G>A		intron_variant	Intron 1 of 5	ENST00000692063.1	NP_001308795.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF600	ENST00000692063.1	c.-643+1747G>A		intron_variant	Intron 1 of 5		NM_001321866.4	ENSP00000509267.1

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

African (AFR) AF: 0.120 AC: 4966 AN: 41526

American (AMR) AF: 0.153 AC: 2345 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 581 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5184

South Asian (SAS) AF: 0.0632 AC: 305 AN: 4828

European-Finnish (FIN) AF: 0.133 AC: 1406 AN: 10598

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11482 AN: 67988

Other (OTH) AF: 0.160 AC: 339 AN: 2114

Alfa AF: 0.155 Hom.: 4298

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
PhyloP100		-1.2
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: rs10407762; hg19: chr19-53288101;