19-51968311-C-T

Position:

• chr19-51968311-C-T

Variant summary

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

The ENST00000243644.9(ZNF350):​c.238+267G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 151,998 control chromosomes in the GnomAD database, including 5,008 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 0.24 (5008 hom., cov: 32)
• Consequence: ZNF350 ENST00000243644.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF350	NM_021632.4	c.238+267G>A		intron_variant		ENST00000243644.9	NP_067645.3
ZNF350-AS1	NR_103847.1	n.103-8080C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF350	ENST00000243644.9	c.238+267G>A		intron_variant		1	NM_021632.4	ENSP00000243644	P1
ZNF350-AS1	ENST00000595010.4	n.121-8080C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35728 AN: 151880 Hom.: 4980 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.216

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.236 AC: 35818 AN: 151998 Hom.: 5008 Cov.: 32 AF XY: 0.240 AC XY: 17828 AN XY: 74286

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.220

Alfa AF: 0.186 Hom.: 1329

Bravo AF: 0.233

Asia WGS AF: 0.308 AC: 1070 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	0.16
DANN	Benign	0.74

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: rs2278416; hg19: chr19-52471564;