15-25120022-CACAG-CACAGACAG

Variant names:

• chr15-25120022-C-CACAG
• rs16416
• ENST00000626200.3:n.1347_1350dupGACA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000626200.3(SNHG14):​n.1347_1350dupGACA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: SNHG14 ENST00000626200.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 3 publications found

Genes affected

SNHG14 (HGNC:37462): (small nucleolar RNA host gene 14) This gene is located within the Prader-Willi critical region and produces a long, spliced paternally-imprinted RNA that initiates within a common upstream promoter region shared by the SNRPN (small nuclear ribonucleoprotein polypeptide N) and SNURF genes. This transcript serves as a host RNA for the small nucleolar RNA, C/D box 115 and 116 clusters. This RNA extends in antisense into the region of the ubiquitin protein ligase E3A gene (UBE3A), and is thought to regulate imprinted expression of UBE3A in the brain. This transcript undergoes extensive alternative splicing, and may initiate and terminate at multiple locations within this genomic region. The full-length structure of all splice forms is not determined. [provided by RefSeq, Mar 2017]

IPW (HGNC:6109): (imprinted in Prader-Willi syndrome) This gene is non-protein coding, is expressed exclusively from the paternal allele, and may play a role in the imprinting process. Mutations in this gene are associated with Prader-Willi syndrome. [provided by RefSeq, May 2010]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000626200.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IPW	NR_023915.1		n.2048_2051dupGACA		non_coding_transcript_exon	Exon 3 of 3
	SNHG14	NR_146177.1		n.10396+1644_10396+1647dupGACA		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG14	ENST00000626200.3	TSL:1	n.1347_1350dupGACA		non_coding_transcript_exon	Exon 5 of 5
	SNHG14	ENST00000549804.7	TSL:5	n.5394_5397dupGACA		non_coding_transcript_exon	Exon 33 of 33
	SNHG14	ENST00000640631.2	TSL:5	n.12668_12671dupGACA		non_coding_transcript_exon	Exon 38 of 38

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs16416; hg19: chr15-25365169;