11-125891482-T-TA

Variant names:

• chr11-125891482-T-TA
• rs886047939
• NM_001134793.2:c.-26+10_-26+11insA

Variant summary

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

The NM_001134793.2(HYLS1):​c.-26+10_-26+11insA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0067 (0 hom., cov: 14)
  • Failed GnomAD Quality Control
• Consequence: HYLS1 NM_001134793.2 intron
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.201

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HYLS1	NM_001134793.2	c.-26+10_-26+11insA		intron_variant	Intron 2 of 2	ENST00000425380.7	NP_001128265.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HYLS1	ENST00000425380.7	c.-26+10_-26+11insA		intron_variant	Intron 2 of 2	3	NM_001134793.2	ENSP00000414884.2
HYLS1	ENST00000356438.7	c.-81+10_-81+11insA		intron_variant	Intron 2 of 3	5		ENSP00000348815.3
HYLS1	ENST00000526028.1	c.-26+10_-26+11insA		intron_variant	Intron 2 of 2	5		ENSP00000436833.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 76 AN: 11270 Hom.: 0 Cov.: 14 FAILED QC

Gnomad AFR AF: 0.00727

Gnomad AMI AF: 0.0303

Gnomad AMR AF: 0.00460

Gnomad ASJ AF: 0.00515

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.00417

Gnomad FIN AF: 0.0156

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00555

Gnomad OTH AF: 0.00820

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00674 AC: 76 AN: 11270 Hom.: 0 Cov.: 14 AF XY: 0.00601 AC XY: 33 AN XY: 5492

Gnomad4 AFR AF: 0.00727

Gnomad4 AMR AF: 0.00460

Gnomad4 ASJ AF: 0.00515

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.00417

Gnomad4 FIN AF: 0.0156

Gnomad4 NFE AF: 0.00555

Gnomad4 OTH AF: 0.00820

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hydrolethalus syndrome Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs886047939; hg19: chr11-125761377;