rs3900738

chr2-200999080-C-Achr2-200999080-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001321623.1(HYCC2):c.531-1540G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,902 control chromosomes in the GnomAD database, including 8,265 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 0.28 (8265 hom., cov: 31)
• Consequence: HYCC2 NM_001321623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HYCC2	NM_001321623.1	c.531-1540G>T		intron_variant		ENST00000681958.1
LOC105373835	XR_007088050.1	n.200-9906C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HYCC2	ENST00000681958.1	c.531-1540G>T		intron_variant			NM_001321623.1	P3
	ENST00000413848.1	n.369-9906C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42219 AN: 151784 Hom.: 8252 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.00946

Gnomad SAS AF: 0.0838

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.278 AC: 42277 AN: 151902 Hom.: 8265 Cov.: 31 AF XY: 0.273 AC XY: 20277 AN XY: 74222

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.00948

Gnomad4 SAS AF: 0.0839

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.258

Alfa AF: 0.226 Hom.: 1160

Bravo AF: 0.293

Asia WGS AF: 0.0810 AC: 283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.93
Dann	Benign	0.37

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

Publications

LitVar

Other links and lift over

dbSNP: rs3900738; hg19: chr2-201863803;