rs13417843

Variant names:

• chr2-201048706-C-G
• rs13417843
• NM_001321623.1:c.-128-3113G>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.-128-3113G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,788 control chromosomes in the GnomAD database, including 4,457 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 0.22 (4457 hom., cov: 30)
• Consequence: HYCC2 NM_001321623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 7 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HYCC2	NM_001321623.1	c.-128-3113G>C		intron_variant	Intron 1 of 12	ENST00000681958.1	NP_001308552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HYCC2	ENST00000681958.1	c.-128-3113G>C		intron_variant	Intron 1 of 12		NM_001321623.1	ENSP00000507218.1

Frequencies

GnomAD3 genomes AF: 0.218 AC: 32991 AN: 151672 Hom.: 4450 Cov.: 30

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00847

Gnomad SAS AF: 0.0708

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.218 AC: 33033 AN: 151788 Hom.: 4457 Cov.: 30 AF XY: 0.213 AC XY: 15826 AN XY: 74176

African (AFR) AF: 0.376 AC: 15554 AN: 41338

American (AMR) AF: 0.164 AC: 2502 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 744 AN: 3466

East Asian (EAS) AF: 0.00849 AC: 44 AN: 5182

South Asian (SAS) AF: 0.0709 AC: 341 AN: 4812

European-Finnish (FIN) AF: 0.165 AC: 1730 AN: 10512

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11523 AN: 67914

Other (OTH) AF: 0.206 AC: 433 AN: 2106

Alfa AF: 0.203 Hom.: 476

Bravo AF: 0.227

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.58
PhyloP100		-0.69
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs13417843; hg19: chr2-201913429;