rs16416

Variant names:

• chr15-25120022-CACAG-C
• rs16416
• ENST00000626200.3:n.1347_1350delGACA

Your query was ambiguous. Multiple possible variants found:

• chr15-25120022-CACAG-C
• chr15-25120022-CACAG-CACAGACAG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000626200.3(SNHG14):​n.1347_1350delGACA 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: 𝑓 0.52 (21750 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: SNHG14 ENST00000626200.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IPW	NR_023915.1	n.2048_2051delGACA		non_coding_transcript_exon_variant	Exon 3 of 3
SNHG14	NR_146177.1	n.10396+1644_10396+1647delGACA		intron_variant	Intron 61 of 147

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNHG14	ENST00000626200.3	n.1347_1350delGACA		non_coding_transcript_exon_variant	Exon 5 of 5	1
SNHG14	ENST00000549804.7	n.5394_5397delGACA		non_coding_transcript_exon_variant	Exon 33 of 33	5
SNHG14	ENST00000640631.2	n.12668_12671delGACA		non_coding_transcript_exon_variant	Exon 38 of 38	5

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78309 AN: 151472 Hom.: 21757 Cov.: 0

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.517 AC: 78306 AN: 151590 Hom.: 21750 Cov.: 0 AF XY: 0.513 AC XY: 37955 AN XY: 74004

African (AFR) AF: 0.327 AC: 13550 AN: 41404

American (AMR) AF: 0.522 AC: 7937 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2109 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1158 AN: 5170

South Asian (SAS) AF: 0.540 AC: 2600 AN: 4814

European-Finnish (FIN) AF: 0.602 AC: 6311 AN: 10476

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.632 AC: 42808 AN: 67760

Other (OTH) AF: 0.518 AC: 1088 AN: 2102

Alfa AF: 0.564 Hom.: 3071

Bravo AF: 0.500

Asia WGS AF: 0.385 AC: 1339 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1

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;