2-201025028-C-T

Variant names:

• chr2-201025028-C-T
• rs7591472
• NM_001321623.1:c.-30-989G>A

Variant summary

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

The NM_001321623.1(HYCC2):​c.-30-989G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 151,908 control chromosomes in the GnomAD database, including 2,345 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 (2345 hom., cov: 31)
• Consequence: HYCC2 NM_001321623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HYCC2	NM_001321623.1	MANE Select	c.-30-989G>A		intron	N/A	NP_001308552.1	A0A804HIT6
	HYCC2	NM_001321624.1		c.-30-989G>A		intron	N/A	NP_001308553.1	A0A804HIT6
	HYCC2	NM_001321625.2		c.-30-989G>A		intron	N/A	NP_001308554.1	A0A804HIT6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HYCC2	ENST00000681958.1	MANE Select	c.-30-989G>A		intron	N/A	ENSP00000507218.1	A0A804HIT6
	HYCC2	ENST00000418596.7	TSL:1	c.-30-989G>A		intron	N/A	ENSP00000393667.2	Q8IXS8
	HYCC2	ENST00000286181.7	TSL:1	n.-30-989G>A		intron	N/A	ENSP00000286181.3	F8W7X4

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25598 AN: 151792 Hom.: 2343 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00849

Gnomad SAS AF: 0.0703

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.169 AC: 25615 AN: 151908 Hom.: 2345 Cov.: 31 AF XY: 0.166 AC XY: 12295 AN XY: 74268

African (AFR) AF: 0.208 AC: 8630 AN: 41406

American (AMR) AF: 0.144 AC: 2189 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3464

East Asian (EAS) AF: 0.00851 AC: 44 AN: 5172

South Asian (SAS) AF: 0.0704 AC: 339 AN: 4814

European-Finnish (FIN) AF: 0.165 AC: 1744 AN: 10558

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11405 AN: 67946

Other (OTH) AF: 0.170 AC: 358 AN: 2104

Alfa AF: 0.164 Hom.: 280

Bravo AF: 0.171

Asia WGS AF: 0.0550 AC: 191 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	0.36
DANN	Benign	0.14
PhyloP100		-1.7
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: rs7591472; hg19: chr2-201889751;