rs3900738

Variant names:

• chr2-200999080-C-A
• rs3900738
• NM_001321623.1:c.531-1540G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-200999080-C-A
• chr2-200999080-C-G

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HYCC2	NM_001321623.1	MANE Select	c.531-1540G>T		intron	N/A	NP_001308552.1
	HYCC2	NM_001321624.1		c.531-1540G>T		intron	N/A	NP_001308553.1
	HYCC2	NM_001321625.2		c.531-1540G>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.531-1540G>T		intron	N/A	ENSP00000507218.1
	HYCC2	ENST00000418596.7	TSL:1	c.531-1540G>T		intron	N/A	ENSP00000393667.2
	HYCC2	ENST00000286181.7	TSL:1	n.*284-1540G>T		intron	N/A	ENSP00000286181.3

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

African (AFR) AF: 0.551 AC: 22812 AN: 41384

American (AMR) AF: 0.187 AC: 2849 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 827 AN: 3468

East Asian (EAS) AF: 0.00948 AC: 49 AN: 5170

South Asian (SAS) AF: 0.0839 AC: 404 AN: 4816

European-Finnish (FIN) AF: 0.181 AC: 1906 AN: 10538

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12694 AN: 67960

Other (OTH) AF: 0.258 AC: 544 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.93
DANN	Benign	0.37
PhyloP100		0.11
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: rs3900738; hg19: chr2-201863803;