rs918442

Variant names:

• chr19-20411294-A-C
• rs918442
• ENST00000541160.8:n.209-2249T>G

Variant summary

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

The ENST00000541160.8(ENSG00000291130):​n.209-2249T>G variant causes a intron 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: ENSG00000291130 ENST00000541160.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321
• Publications: 4 publications found

Genes affected

ENSG00000291130 (HGNC:):

ZNF826P (HGNC:33875): (zinc finger protein 826, pseudogene) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF826P	NR_036455.1	n.181-2270T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291130	ENST00000541160.8	n.209-2249T>G		intron_variant	Intron 1 of 2	1
ENSG00000291130	ENST00000542380.7	n.213+13492T>G		intron_variant	Intron 1 of 2	1
ENSG00000291130	ENST00000597334.4	n.209-2249T>G		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.452 AC: 18721 AN: 41464

American (AMR) AF: 0.494 AC: 7558 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1319 AN: 3464

East Asian (EAS) AF: 0.599 AC: 3097 AN: 5174

South Asian (SAS) AF: 0.404 AC: 1946 AN: 4816

European-Finnish (FIN) AF: 0.421 AC: 4458 AN: 10586

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.374 AC: 25411 AN: 67960

Other (OTH) AF: 0.399 AC: 843 AN: 2112

Alfa AF: 0.389 Hom.: 6079

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs918442; hg19: chr19-20522103;