2-201060065-G-T

Variant names:

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

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>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.15 (1182 hom., cov: 21)
  • Failed GnomAD Quality Control
• 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=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HYCC2	NM_001321623.1	c.-129+11545C>A		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.-129+11545C>A		intron_variant	Intron 1 of 12		NM_001321623.1	ENSP00000507218.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 19939 AN: 130118 Hom.: 1177 Cov.: 21

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.00831

Gnomad SAS AF: 0.0694

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.159

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.153 AC: 19956 AN: 130234 Hom.: 1182 Cov.: 21 AF XY: 0.148 AC XY: 9259 AN XY: 62610

African (AFR) AF: 0.183 AC: 6503 AN: 35486

American (AMR) AF: 0.126 AC: 1644 AN: 13084

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 641 AN: 3140

East Asian (EAS) AF: 0.00833 AC: 33 AN: 3962

South Asian (SAS) AF: 0.0686 AC: 247 AN: 3598

European-Finnish (FIN) AF: 0.124 AC: 913 AN: 7392

Middle Eastern (MID) AF: 0.105 AC: 28 AN: 266

European-Non Finnish (NFE) AF: 0.158 AC: 9564 AN: 60696

Other (OTH) AF: 0.158 AC: 282 AN: 1788

Alfa AF: 0.0968 Hom.: 189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.34
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: rs7590522; hg19: chr2-201924788;