2-201060065-G-A

Variant names:

• chr2-201060065-G-A
• rs7590522
• NM_001321623.1:c.-129+11545C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001321623.1(HYCC2):​c.-129+11545C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000161 in 130,278 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00016 (0 hom., cov: 21)
• Consequence: HYCC2 NM_001321623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341
• Publications: 6 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

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.-129+11545C>T		intron	N/A	NP_001308552.1
	HYCC2	NM_001321624.1		c.-31+11545C>T		intron	N/A	NP_001308553.1
	HYCC2	NM_001321625.2		c.-129+11389C>T		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.-129+11545C>T		intron	N/A	ENSP00000507218.1
	HYCC2	ENST00000418596.7	TSL:1	c.-129+11545C>T		intron	N/A	ENSP00000393667.2
	HYCC2	ENST00000286181.7	TSL:1	n.-129+11545C>T		intron	N/A	ENSP00000286181.3

Frequencies

GnomAD3 genomes AF: 0.000161 AC: 21 AN: 130278 Hom.: 0 Cov.: 21

Gnomad AFR AF: 0.0000282

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00145

Gnomad ASJ AF: 0.000318

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000161 AC: 21 AN: 130278 Hom.: 0 Cov.: 21 AF XY: 0.000208 AC XY: 13 AN XY: 62580

African (AFR) AF: 0.0000282 AC: 1 AN: 35484

American (AMR) AF: 0.00145 AC: 19 AN: 13070

Ashkenazi Jewish (ASJ) AF: 0.000318 AC: 1 AN: 3140

East Asian (EAS) AF: 0.00 AC: 0 AN: 3972

South Asian (SAS) AF: 0.00 AC: 0 AN: 3594

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7400

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 286

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 60734

Other (OTH) AF: 0.00 AC: 0 AN: 1776

Alfa AF: 0.00 Hom.: 189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.82
PhyloP100		-0.34

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: rs7590522; hg19: chr2-201924788;