rs1017379

Variant names:

• chr19-51954053-C-T
• rs1017379
• ENST00000595010.5:n.124+4818C>T

Variant summary

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

The ENST00000595010.5(ZNF350-AS1):​n.124+4818C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,052 control chromosomes in the GnomAD database, including 4,159 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 0.22 (4159 hom., cov: 32)
• Consequence: ZNF350-AS1 ENST00000595010.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 11 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000595010.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF350-AS1	NR_103847.1		n.102+4818C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF350-AS1	ENST00000595010.5	TSL:1	n.124+4818C>T		intron	N/A
	ZNF350-AS1	ENST00000600253.1	TSL:4	n.102+4818C>T		intron	N/A
	ZNF350-AS1	ENST00000658402.1		n.91+4818C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33403 AN: 151936 Hom.: 4134 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.220 AC: 33483 AN: 152052 Hom.: 4159 Cov.: 32 AF XY: 0.225 AC XY: 16725 AN XY: 74326

African (AFR) AF: 0.324 AC: 13416 AN: 41426

American (AMR) AF: 0.185 AC: 2821 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1154 AN: 5176

South Asian (SAS) AF: 0.284 AC: 1370 AN: 4826

European-Finnish (FIN) AF: 0.253 AC: 2670 AN: 10564

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10759 AN: 67996

Other (OTH) AF: 0.212 AC: 447 AN: 2112

Alfa AF: 0.171 Hom.: 3061

Bravo AF: 0.216

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.7
DANN	Benign	0.50
PhyloP100		0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1017379; hg19: chr19-52457306;