rs4986770

Positions:

• chr19-51964781-G-A

Variant summary

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

The ENST00000243644.9(ZNF350):​c.*73C>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 0.0758 in 1,500,484 control chromosomes in the GnomAD database, including 5,551 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 0.079 (544 hom., cov: 33)
  • Exomes 𝑓: 0.076 (5007 hom.)
• Consequence: ZNF350 ENST00000243644.9 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF350	NM_021632.4	c.*73C>T		3_prime_UTR_variant	5/5	ENST00000243644.9	NP_067645.3
ZNF350-AS1	NR_103847.1	n.103-11610G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF350	ENST00000243644.9	c.*73C>T		3_prime_UTR_variant	5/5	1	NM_021632.4	ENSP00000243644	P1
ZNF350-AS1	ENST00000595010.4	n.121-11610G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0785 AC: 11941 AN: 152106 Hom.: 545 Cov.: 33

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.0894

GnomAD4 exome AF: 0.0755 AC: 101860 AN: 1348258 Hom.: 5007 Cov.: 22 AF XY: 0.0794 AC XY: 52823 AN XY: 665076

Gnomad4 AFR exome AF: 0.0957

Gnomad4 AMR exome AF: 0.0510

Gnomad4 ASJ exome AF: 0.0771

Gnomad4 EAS exome AF: 0.0597

Gnomad4 SAS exome AF: 0.221

Gnomad4 FIN exome AF: 0.0584

Gnomad4 NFE exome AF: 0.0664

Gnomad4 OTH exome AF: 0.0854

GnomAD4 genome AF: 0.0785 AC: 11950 AN: 152226 Hom.: 544 Cov.: 33 AF XY: 0.0806 AC XY: 5997 AN XY: 74420

Gnomad4 AFR AF: 0.0900

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.0621

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.0578

Gnomad4 NFE AF: 0.0686

Gnomad4 OTH AF: 0.0889

Alfa AF: 0.0723 Hom.: 423

Bravo AF: 0.0771

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.35

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: rs4986770; hg19: chr19-52468034;