Variant chr7-22941310-A-AAC details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_032581.4(HYCC1):c.*4278_*4279insGT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.39 ( 11663 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

HYCC1
NM_032581.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.28

Variant links:

Genes affected

HYCC1 (HGNC:24587): (hyccin PI4KA lipid kinase complex subunit 1) The protein encoded by this gene may play a part in the beta-catenin/Lef signaling pathway. Expression of this gene is down-regulated by beta-catenin. Defects in this gene are a cause of hypomyelination with congenital cataract (HCC). [provided by RefSeq, Oct 2008]

HYCC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 7-22941310-A-AAC is Benign according to our data. Variant chr7-22941310-A-AAC is described in ClinVar as [Benign]. Clinvar id is 359713.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HYCC1	NM_032581.4 linkuse as main transcript	c.4278_4279insGT		3_prime_UTR_variant	11/11	ENST00000432176.7	NP_115970.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
HYCC1	ENST00000432176.7 linkuse as main transcript	c.4278_4279insGT	3_prime_UTR_variant	11/11	1	NM_032581.4	ENSP00000403396	Q9BYI3-1
HYCC1	ENST00000440481.6 linkuse as main transcript	c.4880_4881insGT	3_prime_UTR_variant	11/11	1		ENSP00000397168
HYCC1	ENST00000465661.2 linkuse as main transcript	n.1182+18945_1182+18946insGT	intron_variant, non_coding_transcript_variant		3
HYCC1	ENST00000679826.1 linkuse as main transcript		downstream_gene_variant				ENSP00000505460

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59617

AN:

151748

Hom.:

11651

Cov.:

show subpopulations

Gnomad AFR

AF:

0.387

Gnomad AMI

AF:

0.458

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.467

Gnomad EAS

AF:

0.504

Gnomad SAS

AF:

0.454

Gnomad FIN

AF:

0.364

Gnomad MID

AF:

0.325

Gnomad NFE

AF:

0.390

Gnomad OTH

AF:

0.361

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

GnomAD4 genome

AF:

0.393

AC:

59665

AN:

151866

Hom.:

11663

Cov.:

AF XY:

0.392

AC XY:

29091

AN XY:

74204

show subpopulations

Gnomad4 AFR

AF:

0.387

Gnomad4 AMR

AF:

0.370

Gnomad4 ASJ

AF:

0.467

Gnomad4 EAS

AF:

0.505

Gnomad4 SAS

AF:

0.454

Gnomad4 FIN

AF:

0.364

Gnomad4 NFE

AF:

0.390

Gnomad4 OTH

AF:

0.364

Alfa

AF:

0.384

Hom.:

1354

Bravo

AF:

0.396

Asia WGS

AF:

0.475

AC:

1651

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Hypomyelination and Congenital Cataract

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