7-22941310-A-AAC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.28

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]

ACMG classification

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	UniProt
HYCC1	NM_032581.4	c.*4278_*4279insGT		3_prime_UTR_variant	11/11	ENST00000432176.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HYCC1	ENST00000432176.7	c.*4278_*4279insGT		3_prime_UTR_variant	11/11	1	NM_032581.4
HYCC1	ENST00000440481.6	c.*4880_*4881insGT		3_prime_UTR_variant	11/11	1
HYCC1	ENST00000465661.2	n.1182+18945_1182+18946insGT		intron_variant, non_coding_transcript_variant		3
HYCC1	ENST00000679826.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59617 AN: 151748 Hom.: 11651 Cov.: 0

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: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.393 AC: 59665 AN: 151866 Hom.: 11663 Cov.: 0 AF XY: 0.392 AC XY: 29091 AN XY: 74204

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

Submissions by phenotype

Hypomyelination and Congenital Cataract Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35708583; hg19: chr7-22980929;