2-201060065-G-T

Position:

• chr2-201060065-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001321623.1(HYCC2):​c.-129+11545C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.15 (1182 hom., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: HYCC2 NM_001321623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341

Genes affected

HYCC2 (HGNC:28593): (hyccin PI4KA lipid kinase complex subunit 2) Predicted to be involved in phosphatidylinositol phosphate biosynthetic process and protein localization to plasma membrane. Predicted to be located in cytosol. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HYCC2	NM_001321623.1	c.-129+11545C>A		intron_variant		ENST00000681958.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HYCC2	ENST00000681958.1	c.-129+11545C>A		intron_variant			NM_001321623.1	P3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 19939 AN: 130118 Hom.: 1177 Cov.: 21 FAILED QC

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.00831

Gnomad SAS AF: 0.0694

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.159

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.153 AC: 19956 AN: 130234 Hom.: 1182 Cov.: 21 AF XY: 0.148 AC XY: 9259 AN XY: 62610

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.00833

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.158

Alfa AF: 0.0968 Hom.: 189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.58

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: rs7590522; hg19: chr2-201924788;