rs237743

chr20-49286482-G-A

Variant summary

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

The NR_003604.3(ZFAS1):n.793-2563G>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 0.223 in 152,032 control chromosomes in the GnomAD database, including 4,020 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 (4020 hom., cov: 31)
• Consequence: ZFAS1 NR_003604.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

ZFAS1 (HGNC:33101): (ZNFX1 antisense RNA 1) This gene represents a snoRNA host gene that produces a non-coding RNA. Increased expression or amplification of this locus is associated with cancer progression and metastasis. This transcript regulates expression of genes involved in differentiation. It may act a molecular sponge for microRNAs. Alternatively spliced transcript variants have been observed. [provided by RefSeq, Dec 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFAS1	NR_003604.3	n.793-2563G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZFAS1	ENST00000620594.2	n.328+5518G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33870 AN: 151914 Hom.: 4014 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0513

Gnomad SAS AF: 0.0867

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.223 AC: 33910 AN: 152032 Hom.: 4020 Cov.: 31 AF XY: 0.217 AC XY: 16130 AN XY: 74292

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0513

Gnomad4 SAS AF: 0.0880

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.177

Alfa AF: 0.207 Hom.: 4843

Bravo AF: 0.219

Asia WGS AF: 0.102 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.6
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs237743; hg19: chr20-47903019;