rs2200578

Positions:

• chr2-99259781-C-T

Variant summary

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

The ENST00000424491.5(ENSG00000241962):​n.*292+43667C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,764 control chromosomes in the GnomAD database, including 2,583 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 0.17 (2583 hom., cov: 31)
• Consequence: ENSG00000241962 ENST00000424491.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

ENSG00000241962 (HGNC:):

LYG2 (HGNC:29615): (lysozyme g2) The protein encoded by this gene contains a SLT domain, a protein domain present in bacterial lytic transglycosylase (SLT) and in eukaryotic lysozymes (GEWL). SLT domain catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyglucosamine (GlcNAc). [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LYG2	XM_017003751.3	c.-4327G>A		5_prime_UTR_premature_start_codon_gain_variant	1/7		XP_016859240.1
LYG2	XM_017003751.3	c.-4327G>A		5_prime_UTR_variant	1/7		XP_016859240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000241962	ENST00000424491.5	n.*292+43667C>T		intron_variant		2		ENSP00000390891.1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26068 AN: 151644 Hom.: 2582 Cov.: 31

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.172 AC: 26082 AN: 151764 Hom.: 2583 Cov.: 31 AF XY: 0.174 AC XY: 12902 AN XY: 74136

Gnomad4 AFR AF: 0.0835

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.183

Alfa AF: 0.187 Hom.: 2619

Bravo AF: 0.173

Asia WGS AF: 0.182 AC: 631 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.58

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: rs2200578; hg19: chr2-99876244;