19-51964569-G-A

Position:

• chr19-51964569-G-A

Variant summary

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

The NM_021632.4(ZNF350):​c.*285C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 427,122 control chromosomes in the GnomAD database, including 4,474 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 0.12 (1314 hom., cov: 32)
  • Exomes 𝑓: 0.14 (3160 hom.)
• Consequence: ZNF350 NM_021632.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535

Genes affected

ZNF350 (HGNC:16656): (zinc finger protein 350) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nuclear body. Part of transcription repressor complex. [provided by Alliance of Genome Resources, Apr 2022]

ZNF350-AS1 (HGNC:48598): (ZNF350 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF350	NM_021632.4	c.*285C>T		3_prime_UTR_variant	5/5	ENST00000243644.9	NP_067645.3
ZNF350-AS1	NR_103847.1	n.103-11822G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF350	ENST00000243644.9	c.*285C>T		3_prime_UTR_variant	5/5	1	NM_021632.4	ENSP00000243644	P1
ZNF350-AS1	ENST00000595010.4	n.121-11822G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17863 AN: 151956 Hom.: 1315 Cov.: 32

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.114

GnomAD4 exome AF: 0.142 AC: 39044 AN: 275048 Hom.: 3160 Cov.: 3 AF XY: 0.146 AC XY: 20867 AN XY: 142876

Gnomad4 AFR exome AF: 0.0421

Gnomad4 AMR exome AF: 0.139

Gnomad4 ASJ exome AF: 0.0970

Gnomad4 EAS exome AF: 0.228

Gnomad4 SAS exome AF: 0.228

Gnomad4 FIN exome AF: 0.160

Gnomad4 NFE exome AF: 0.129

Gnomad4 OTH exome AF: 0.119

GnomAD4 genome AF: 0.117 AC: 17868 AN: 152074 Hom.: 1314 Cov.: 32 AF XY: 0.124 AC XY: 9203 AN XY: 74336

Gnomad4 AFR AF: 0.0467

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.116

Alfa AF: 0.131 Hom.: 1087

Bravo AF: 0.104

Asia WGS AF: 0.253 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.28

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: rs2278414; hg19: chr19-52467822;