20-49286482-G-C

Variant names:

• chr20-49286482-G-C
• rs237743
• ENST00000326677.10:n.329-2563G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000326677.10(ZFAS1):​n.329-2563G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: ZFAS1 ENST00000326677.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000326677.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFAS1	NR_003604.3		n.793-2563G>C		intron	N/A
	ZFAS1	NR_003605.2		n.474-2563G>C		intron	N/A
	ZFAS1	NR_003606.3		n.645-2563G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFAS1	ENST00000326677.10	TSL:1	n.329-2563G>C		intron	N/A
	ZFAS1	ENST00000371743.8	TSL:1	n.793-2563G>C		intron	N/A
	ZFAS1	ENST00000417721.6	TSL:1	n.645-2563G>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.41
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs237743; hg19: chr20-47903019;