rs6719992

Variant names:

• chr2-201007255-A-G
• rs6719992
• NM_001321623.1:c.530+1718T>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.530+1718T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,064 control chromosomes in the GnomAD database, including 4,372 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 (4372 hom., cov: 31)
• Consequence: HYCC2 NM_001321623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• 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]

ENSG00000183308 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HYCC2	NM_001321623.1	c.530+1718T>C		intron_variant	Intron 7 of 12	ENST00000681958.1	NP_001308552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HYCC2	ENST00000681958.1	c.530+1718T>C		intron_variant	Intron 7 of 12		NM_001321623.1	ENSP00000507218.1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32788 AN: 151946 Hom.: 4365 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00847

Gnomad SAS AF: 0.0710

Gnomad FIN AF: 0.164

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: 0.216 AC: 32830 AN: 152064 Hom.: 4372 Cov.: 31 AF XY: 0.211 AC XY: 15693 AN XY: 74324

African (AFR) AF: 0.370 AC: 15324 AN: 41440

American (AMR) AF: 0.164 AC: 2501 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 743 AN: 3462

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

South Asian (SAS) AF: 0.0710 AC: 343 AN: 4830

European-Finnish (FIN) AF: 0.164 AC: 1739 AN: 10582

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

European-Non Finnish (NFE) AF: 0.170 AC: 11540 AN: 67990

Other (OTH) AF: 0.206 AC: 435 AN: 2110

Alfa AF: 0.202 Hom.: 470

Bravo AF: 0.225

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	-0.93
CADD	Benign	0.057
DANN	Benign	0.48
PhyloP100		-0.14
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: rs6719992; hg19: chr2-201871978;