chr2-201016954-A-G

Position:

• chr2-201016954-A-G

Variant summary

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

The NM_001321623.1(HYCC2):​c.333+37T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 1,589,454 control chromosomes in the GnomAD database, including 24,965 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 (4463 hom., cov: 32)
  • Exomes 𝑓: 0.16 (20502 hom.)
• Consequence: HYCC2 NM_001321623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

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]

LOC105373835 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HYCC2	NM_001321623.1	c.333+37T>C		intron_variant		ENST00000681958.1	NP_001308552.1
LOC105373835	XR_007088050.1	n.1482A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HYCC2	ENST00000681958.1	c.333+37T>C		intron_variant			NM_001321623.1	ENSP00000507218	P3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32980 AN: 151980 Hom.: 4456 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00847

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.208

GnomAD3 exomes AF: 0.154 AC: 37401 AN: 242392 Hom.: 3765 AF XY: 0.150 AC XY: 19784 AN XY: 131774

Gnomad AFR exome AF: 0.392

Gnomad AMR exome AF: 0.110

Gnomad ASJ exome AF: 0.204

Gnomad EAS exome AF: 0.00576

Gnomad SAS exome AF: 0.0790

Gnomad FIN exome AF: 0.168

Gnomad NFE exome AF: 0.170

Gnomad OTH exome AF: 0.171

GnomAD4 exome AF: 0.161 AC: 231779 AN: 1437356 Hom.: 20502 Cov.: 25 AF XY: 0.159 AC XY: 113652 AN XY: 715364

Gnomad4 AFR exome AF: 0.381

Gnomad4 AMR exome AF: 0.117

Gnomad4 ASJ exome AF: 0.207

Gnomad4 EAS exome AF: 0.00350

Gnomad4 SAS exome AF: 0.0789

Gnomad4 FIN exome AF: 0.170

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.165

GnomAD4 genome AF: 0.217 AC: 33023 AN: 152098 Hom.: 4463 Cov.: 32 AF XY: 0.213 AC XY: 15827 AN XY: 74376

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.00849

Gnomad4 SAS AF: 0.0708

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.206

Alfa AF: 0.158 Hom.: 748

Bravo AF: 0.227

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	-0.83
CADD	Benign	9.7
DANN	Benign	0.70

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: rs13405753; hg19: chr2-201881677;