Variant 11-125891423-G-GTTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001134793.2(HYLS1):c.-67_-65dup variant causes a splice region, 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00075 ( 1 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

HYLS1
NM_001134793.2 splice_region, 5_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.440

Variant links:

Genes affected

HYLS1 (HGNC:26558): (HYLS1 centriolar and ciliogenesis associated) This gene encodes a protein localized to the cytoplasm. Mutations in this gene are associated with hydrolethalus syndrome. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Oct 2008]

HYLS1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HYLS1	NM_001134793.2 linkuse as main transcript	c.-67_-65dup		splice_region_variant, 5_prime_UTR_variant	2/3	ENST00000425380.7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
HYLS1	ENST00000425380.7 linkuse as main transcript	c.-67_-65dup	splice_region_variant, 5_prime_UTR_variant	2/3	3	NM_001134793.2	P1
HYLS1	ENST00000356438.7 linkuse as main transcript	c.-122_-120dup	splice_region_variant, 5_prime_UTR_variant	2/4	5		P1
HYLS1	ENST00000526028.1 linkuse as main transcript	c.-67_-65dup	splice_region_variant, 5_prime_UTR_variant	2/3	5		P1

Frequencies

GnomAD3 genomes

AF:

0.000751

AC:

102

AN:

135878

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000331

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000537

Gnomad ASJ

AF:

0.000292

Gnomad EAS

AF:

0.00104

Gnomad SAS

AF:

0.00706

Gnomad FIN

AF:

0.000895

Gnomad MID

AF:

0.00357

Gnomad NFE

AF:

0.000581

Gnomad OTH

AF:

0.00110

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

GnomAD4 genome

AF:

0.000751

AC:

102

AN:

135892

Hom.:

Cov.:

AF XY:

0.000851

AC XY:

AN XY:

64614

show subpopulations

Gnomad4 AFR

AF:

0.000331

Gnomad4 AMR

AF:

0.000537

Gnomad4 ASJ

AF:

0.000292

Gnomad4 EAS

AF:

0.00104

Gnomad4 SAS

AF:

0.00710

Gnomad4 FIN

AF:

0.000895

Gnomad4 NFE

AF:

0.000581

Gnomad4 OTH

AF:

0.00109

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Hydrolethalus syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over