rs10404486

Variant names:

• chr19-52780882-C-G
• rs10404486
• NM_001321866.4:c.-321G>C

Your query was ambiguous. Multiple possible variants found:

• chr19-52780882-C-G
• chr19-52780882-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001321866.4(ZNF600):​c.-321G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ZNF600 NM_001321866.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 23 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321866.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF600	NM_001321866.4	MANE Select	c.-321G>C		5_prime_UTR	Exon 3 of 6	NP_001308795.1	A0A3B3IT03
	ZNF600	NM_001321867.3		c.-19-1975G>C		intron	N/A	NP_001308796.1	A0A3B3IT03
	ZNF600	NM_198457.5		c.-99-1975G>C		intron	N/A	NP_940859.3	Q6ZNG1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF600	ENST00000692063.1	MANE Select	c.-321G>C		5_prime_UTR	Exon 3 of 6	ENSP00000509267.1	A0A3B3IT03
	ZNF600	ENST00000338230.3	TSL:1	c.-99-1975G>C		intron	N/A	ENSP00000344791.2	Q6ZNG1
	ZNF600	ENST00000688329.1		c.-214G>C		5_prime_UTR	Exon 2 of 6	ENSP00000509375.1	A0A3B3IT03

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 5183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.21
PhyloP100		-1.5

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: rs10404486; hg19: chr19-53284135;