rs16836568

Variant names:

• chr2-201015225-A-G
• rs16836568
• NM_001321623.1:c.333+1766T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321623.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HYCC2	NM_001321623.1	MANE Select	c.333+1766T>C		intron	N/A	NP_001308552.1
	HYCC2	NM_001321624.1		c.333+1766T>C		intron	N/A	NP_001308553.1
	HYCC2	NM_001321625.2		c.333+1766T>C		intron	N/A	NP_001308554.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HYCC2	ENST00000681958.1	MANE Select	c.333+1766T>C		intron	N/A	ENSP00000507218.1
	HYCC2	ENST00000418596.7	TSL:1	c.333+1766T>C		intron	N/A	ENSP00000393667.2
	HYCC2	ENST00000286181.7	TSL:1	n.*86+1766T>C		intron	N/A	ENSP00000286181.3

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

African (AFR) AF: 0.380 AC: 15739 AN: 41464

American (AMR) AF: 0.170 AC: 2603 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 824 AN: 3472

East Asian (EAS) AF: 0.00887 AC: 46 AN: 5188

South Asian (SAS) AF: 0.0830 AC: 401 AN: 4830

European-Finnish (FIN) AF: 0.180 AC: 1904 AN: 10574

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12658 AN: 68002

Other (OTH) AF: 0.219 AC: 462 AN: 2112

Alfa AF: 0.204 Hom.: 5353

Bravo AF: 0.237

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.39
PhyloP100		-3.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16836568; hg19: chr2-201879948;