NM_032517.6:c.139+7C>G

Variant names:

• chr10-29292013-C-G
• rs2209788
• NM_032517.6:c.139+7C>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_032517.6(LYZL1):​c.139+7C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000092 (0 hom., cov: 19)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LYZL1 NM_032517.6 splice_region, intron
• Scores: Splicing: ADA: 0.00005281
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• Publications: 2 publications found

Genes affected

LYZL1 (HGNC:30502): (lysozyme like 1) Predicted to enable lysozyme activity. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000305098 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032517.6. 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
	LYZL1	NM_032517.6	MANE Select	c.139+7C>G		splice_region intron	N/A	NP_115906.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYZL1	ENST00000649382.2	MANE Select	c.139+7C>G		splice_region intron	N/A	ENSP00000498092.1	Q6UWQ5-1
	LYZL1	ENST00000375500.8	TSL:1	c.277+7C>G		splice_region intron	N/A	ENSP00000364650.3	Q6UWQ5-2
	LYZL1	ENST00000494304.1	TSL:3	n.82+7C>G		splice_region intron	N/A	ENSP00000434629.1	H0YDZ2

Frequencies

GnomAD3 genomes AF: 0.00000917 AC: 1 AN: 109040 Hom.: 0 Cov.: 19

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000213

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1101094 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 550780

African (AFR) AF: 0.00 AC: 0 AN: 29802

American (AMR) AF: 0.00 AC: 0 AN: 35068

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20296

East Asian (EAS) AF: 0.00 AC: 0 AN: 36084

South Asian (SAS) AF: 0.00 AC: 0 AN: 72592

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44266

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4224

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 811182

Other (OTH) AF: 0.00 AC: 0 AN: 47580

GnomAD4 genome AF: 0.00000917 AC: 1 AN: 109108 Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0 AN XY: 52418

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 32840

American (AMR) AF: 0.00 AC: 0 AN: 10150

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2550

East Asian (EAS) AF: 0.00 AC: 0 AN: 3810

South Asian (SAS) AF: 0.00 AC: 0 AN: 3416

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6914

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 234

European-Non Finnish (NFE) AF: 0.0000213 AC: 1 AN: 47044

Other (OTH) AF: 0.00 AC: 0 AN: 1462

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		-0.19

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000053
dbscSNV1_RF	Benign	0.028
SpliceAI score (max)		0.020		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: rs2209788; hg19: chr10-29580942;