rs237743

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr20-49286482-G-A
• chr20-49286482-G-C
• chr20-49286482-G-T

Variant summary

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

The ENST00000326677.10(ZFAS1):​n.329-2563G>A variant causes a intron 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 ENST00000326677.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 51 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: Benign. The variant received -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.

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>A		intron	N/A
	ZFAS1	NR_003605.2		n.474-2563G>A		intron	N/A
	ZFAS1	NR_003606.3		n.645-2563G>A		intron	N/A

Ensembl Transcripts

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

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

African (AFR) AF: 0.296 AC: 12252 AN: 41430

American (AMR) AF: 0.172 AC: 2633 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3468

East Asian (EAS) AF: 0.0513 AC: 266 AN: 5188

South Asian (SAS) AF: 0.0880 AC: 424 AN: 4818

European-Finnish (FIN) AF: 0.216 AC: 2278 AN: 10568

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.218 AC: 14798 AN: 67970

Other (OTH) AF: 0.177 AC: 374 AN: 2110

Alfa AF: 0.213 Hom.: 11648

Bravo AF: 0.219

Asia WGS AF: 0.102 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.32
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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;