rs366860

Variant names:

• chr20-46512761-A-C
• rs366860
• NM_001353824.2:c.-260T>G

Your query was ambiguous. Multiple possible variants found:

• chr20-46512761-A-C
• chr20-46512761-A-T

Variant summary

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

The NM_001353824.2(ZNF334):​c.-260T>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 0.539 in 152,056 control chromosomes in the GnomAD database, including 22,457 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 0.54 (22455 hom., cov: 32)
  • Exomes 𝑓: 0.75 (2 hom.)
• Consequence: ZNF334 NM_001353824.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70
• Publications: 11 publications found

Genes affected

ZNF334 (HGNC:15806): (zinc finger protein 334) This gene encodes a member of the C2H2 zinc finger family. The encoded protein contains a Krueppel-associated box, fourteen C2H2 zinc finger domains, and four C2H2-type/integrase DNA-binding domains. Decreased expression of this gene may be a marker for rheumatoid arthritis. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001353824.2. 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
	ZNF334	NM_001353824.2	MANE Select	c.-260T>G		5_prime_UTR	Exon 1 of 5	NP_001340753.1	Q9HCZ1
	ZNF334	NM_001353826.2		c.-377T>G		5_prime_UTR	Exon 1 of 5	NP_001340755.1
	ZNF334	NM_001353822.2		c.-410T>G		5_prime_UTR	Exon 1 of 6	NP_001340751.1	A0A087X1P4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF334	ENST00000692313.1	MANE Select	c.-260T>G		5_prime_UTR	Exon 1 of 5	ENSP00000510334.1	Q9HCZ1
	ZNF334	ENST00000347606.8	TSL:1	c.-38-621T>G		intron	N/A	ENSP00000255129.5	Q9HCZ1
	ZNF334	ENST00000938191.1		c.-659T>G		5_prime_UTR	Exon 1 of 4	ENSP00000608250.1

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81861 AN: 151930 Hom.: 22399 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.531

GnomAD4 exome AF: 0.750 AC: 6 AN: 8 Hom.: 2 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 6 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.539 AC: 81973 AN: 152048 Hom.: 22455 Cov.: 32 AF XY: 0.538 AC XY: 40022 AN XY: 74330

African (AFR) AF: 0.638 AC: 26462 AN: 41470

American (AMR) AF: 0.497 AC: 7603 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1792 AN: 3468

East Asian (EAS) AF: 0.361 AC: 1871 AN: 5180

South Asian (SAS) AF: 0.559 AC: 2693 AN: 4816

European-Finnish (FIN) AF: 0.486 AC: 5138 AN: 10564

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34564 AN: 67950

Other (OTH) AF: 0.533 AC: 1125 AN: 2110

Alfa AF: 0.507 Hom.: 54348

Bravo AF: 0.543

Asia WGS AF: 0.513 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.58
PhyloP100		-2.7
Mutation Taster		=299/1	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: rs366860; hg19: chr20-45141400;