chr2-201015225-A-G

Position:

• chr2-201015225-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001321623.1(HYCC2):​c.333+1766T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,124 control chromosomes in the GnomAD database, including 4,786 homozygotes. 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 0.23 (4786 hom., cov: 32)
• Consequence: HYCC2 NM_001321623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08

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]

LOC105373835 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HYCC2	NM_001321623.1	c.333+1766T>C		intron_variant		ENST00000681958.1	NP_001308552.1
LOC105373835	XR_007088050.1	n.316-563A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HYCC2	ENST00000681958.1	c.333+1766T>C		intron_variant			NM_001321623.1	ENSP00000507218	P3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34785 AN: 152006 Hom.: 4779 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.00885

Gnomad SAS AF: 0.0830

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.229 AC: 34829 AN: 152124 Hom.: 4786 Cov.: 32 AF XY: 0.224 AC XY: 16673 AN XY: 74352

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.00887

Gnomad4 SAS AF: 0.0830

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.219

Alfa AF: 0.224 Hom.: 729

Bravo AF: 0.237

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.39

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: rs16836568; hg19: chr2-201879948;