rs13389349

Variant names:

• chr2-201055895-T-C
• rs13389349
• NM_001321623.1:c.-128-10302A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001321623.1(HYCC2):​c.-128-10302A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,518 control chromosomes in the GnomAD database, including 2,360 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 0.17 (2360 hom., cov: 31)
• Consequence: HYCC2 NM_001321623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HYCC2	NM_001321623.1	c.-128-10302A>G		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.-128-10302A>G		intron_variant	Intron 1 of 12		NM_001321623.1	ENSP00000507218.1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25707 AN: 151400 Hom.: 2358 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00865

Gnomad SAS AF: 0.0709

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.129

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.170 AC: 25724 AN: 151518 Hom.: 2360 Cov.: 31 AF XY: 0.167 AC XY: 12342 AN XY: 74052

African (AFR) AF: 0.209 AC: 8640 AN: 41296

American (AMR) AF: 0.145 AC: 2202 AN: 15216

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

East Asian (EAS) AF: 0.00868 AC: 44 AN: 5072

South Asian (SAS) AF: 0.0710 AC: 341 AN: 4804

European-Finnish (FIN) AF: 0.165 AC: 1740 AN: 10532

Middle Eastern (MID) AF: 0.125 AC: 36 AN: 288

European-Non Finnish (NFE) AF: 0.169 AC: 11492 AN: 67834

Other (OTH) AF: 0.171 AC: 359 AN: 2102

Alfa AF: 0.175 Hom.: 315

Bravo AF: 0.172

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.9
DANN	Benign	0.57
PhyloP100		0.30
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: rs13389349; hg19: chr2-201920618;