rs918442

Positions:

• chr19-20411294-A-C

Variant summary

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

The NR_036455.1(ZNF826P):​n.181-2270T>G 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 0.419 in 152,068 control chromosomes in the GnomAD database, including 13,707 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 0.42 (13707 hom., cov: 32)
• Consequence: ZNF826P NR_036455.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF826P	NR_036455.1	n.181-2270T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000541160.7	n.194-2249T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63653 AN: 151948 Hom.: 13687 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.419 AC: 63724 AN: 152068 Hom.: 13707 Cov.: 32 AF XY: 0.426 AC XY: 31647 AN XY: 74326

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.399

Alfa AF: 0.391 Hom.: 5587

Bravo AF: 0.427

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs918442; hg19: chr19-20522103;