Variant chr11-125891423-G-GTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001134793.2(HYLS1):c.-66_-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 Benign (★).

Frequency

Genomes: 𝑓 0.82 ( 45797 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

HYLS1
NM_001134793.2 splice_region, 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B: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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-125891423-G-GTT is Benign according to our data. Variant chr11-125891423-G-GTT is described in ClinVar as [Benign]. Clinvar id is 303351.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HYLS1	NM_001134793.2 linkuse as main transcript	c.-66_-65dup		splice_region_variant, 5_prime_UTR_variant	2/3	ENST00000425380.7	NP_001128265.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
HYLS1	ENST00000425380.7 linkuse as main transcript	c.-66_-65dup	splice_region_variant, 5_prime_UTR_variant	2/3	3	NM_001134793.2	ENSP00000414884	P1
HYLS1	ENST00000356438.7 linkuse as main transcript	c.-121_-120dup	splice_region_variant, 5_prime_UTR_variant	2/4	5		ENSP00000348815	P1
HYLS1	ENST00000526028.1 linkuse as main transcript	c.-66_-65dup	splice_region_variant, 5_prime_UTR_variant	2/3	5		ENSP00000436833	P1

Frequencies

GnomAD3 genomes

AF:

0.820

AC:

111277

AN:

135682

Hom.:

45791

Cov.:

show subpopulations

Gnomad AFR

AF:

0.684

Gnomad AMI

AF:

0.692

Gnomad AMR

AF:

0.890

Gnomad ASJ

AF:

0.870

Gnomad EAS

AF:

0.885

Gnomad SAS

AF:

0.861

Gnomad FIN

AF:

0.841

Gnomad MID

AF:

0.815

Gnomad NFE

AF:

0.871

Gnomad OTH

AF:

0.817

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

GnomAD4 genome

AF:

0.820

AC:

111287

AN:

135696

Hom.:

45797

Cov.:

AF XY:

0.820

AC XY:

52904

AN XY:

64500

show subpopulations

Gnomad4 AFR

AF:

0.684

Gnomad4 AMR

AF:

0.890

Gnomad4 ASJ

AF:

0.870

Gnomad4 EAS

AF:

0.885

Gnomad4 SAS

AF:

0.861

Gnomad4 FIN

AF:

0.841

Gnomad4 NFE

AF:

0.871

Gnomad4 OTH

AF:

0.818

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Hydrolethalus syndrome

Benign:1

Benign, 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