Variant rs16416 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_023915.1(IPW):n.2048_2051del 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

IPW
NR_023915.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.14

Variant links:

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]

SNHG14 links:

IPW (HGNC:):

IPW links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
IPW	NR_023915.1 linkuse as main transcript	n.2048_2051del		non_coding_transcript_exon_variant	3/3
SNHG14	NR_146177.1 linkuse as main transcript	n.10396+1644_10396+1647del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
SNHG14	ENST00000626200.3 linkuse as main transcript	n.1347_1350del	non_coding_transcript_exon_variant	5/5	1
SNHG14	ENST00000549804.7 linkuse as main transcript	n.5394_5397del	non_coding_transcript_exon_variant	33/33	5
SNHG14	ENST00000640631.2 linkuse as main transcript	n.12668_12671del	non_coding_transcript_exon_variant	38/38	5

Frequencies

GnomAD3 genomes

AF:

0.517

AC:

78309

AN:

151472

Hom.:

21757

Cov.:

show subpopulations

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.:

AF XY:

0.513

AC XY:

37955

AN XY:

74004

show subpopulations

Gnomad4 AFR

AF:

0.327

Gnomad4 AMR

AF:

0.522

Gnomad4 ASJ

AF:

0.608

Gnomad4 EAS

AF:

0.224

Gnomad4 SAS

AF:

0.540

Gnomad4 FIN

AF:

0.602

Gnomad4 NFE

AF:

0.632

Gnomad4 OTH

AF:

0.518

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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over