17-12019847-A-T

Position:

• chr17-12019847-A-T

Variant summary

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

The ENST00000579522.1(ENSG00000293152):​n.186+1476T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,144 control chromosomes in the GnomAD database, including 4,074 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 0.23 (4074 hom., cov: 32)
• Consequence: ENST00000579522.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF18	XM_024450911.2	c.-329+1476T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000579522.1	n.186+1476T>A		intron_variant, non_coding_transcript_variant		3
	ENST00000578024.1	n.24+1476T>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34509 AN: 152028 Hom.: 4070 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.227 AC: 34527 AN: 152144 Hom.: 4074 Cov.: 32 AF XY: 0.226 AC XY: 16782 AN XY: 74350

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.233

Alfa AF: 0.129 Hom.: 247

Bravo AF: 0.226

Asia WGS AF: 0.171 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809728; hg19: chr17-11923164;