20-49245566-A-G

Position:

• chr20-49245566-A-G

Variant summary

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

The ENST00000371754.8(ZNFX1):​c.3313-3643T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 151,834 control chromosomes in the GnomAD database, including 34,841 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 0.67 (34841 hom., cov: 30)
• Consequence: ZNFX1 ENST00000371754.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812

Genes affected

ZNFX1 (HGNC:29271): (zinc finger NFX1-type containing 1) Enables RNA binding activity. Predicted to be involved in heterochromatin assembly by small RNA. Predicted to be part of nuclear RNA-directed RNA polymerase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNFX1	ENST00000371754.8	c.3313-3643T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101412 AN: 151716 Hom.: 34834 Cov.: 30

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.668 AC: 101443 AN: 151834 Hom.: 34841 Cov.: 30 AF XY: 0.664 AC XY: 49270 AN XY: 74178

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.668

Alfa AF: 0.660 Hom.: 2155

Bravo AF: 0.647

Asia WGS AF: 0.554 AC: 1925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
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: rs238206; hg19: chr20-47862103;