rs2200578

Variant names:

• chr2-99259781-C-T
• rs2200578
• ENST00000424491.5:n.*292+43667C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424491.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000241962	ENST00000424491.5	TSL:2	n.*292+43667C>T		intron	N/A	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

African (AFR) AF: 0.0835 AC: 3459 AN: 41418

American (AMR) AF: 0.247 AC: 3761 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1339 AN: 5160

South Asian (SAS) AF: 0.125 AC: 598 AN: 4802

European-Finnish (FIN) AF: 0.244 AC: 2540 AN: 10430

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13381 AN: 67922

Other (OTH) AF: 0.183 AC: 386 AN: 2110

Alfa AF: 0.185 Hom.: 6970

Bravo AF: 0.173

Asia WGS AF: 0.182 AC: 631 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.58
PhyloP100		-1.7

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2200578;

hg19: chr2-99876244;