NM_020426.4:c.197C>A

Variant names:

• chr17-35937859-G-T
• rs780416398
• NM_020426.4:c.197C>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020426.4(LYZL6):​c.197C>A​(p.Ala66Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A66V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LYZL6 NM_020426.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 0 publications found

Genes affected

LYZL6 (HGNC:29614): (lysozyme like 6) This gene encodes a member of the C-type lysozyme/alpha-lactalbumin family. C-type lysozymes are bacteriolytic factors that play a role in host defense, whereas alpha-lactalbumins mediate lactose biosynthesis. The encoded protein contains catalytic residues characteristic of C-type lysozymes and may play a role in male reproduction. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jan 2011]

ENSG00000270240 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07008523).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYZL6	NM_020426.4	c.197C>A	p.Ala66Glu	missense_variant	Exon 3 of 5	ENST00000615905.5	NP_065159.1
LYZL6	NM_001199951.3	c.197C>A	p.Ala66Glu	missense_variant	Exon 3 of 5		NP_001186880.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYZL6	ENST00000615905.5	c.197C>A	p.Ala66Glu	missense_variant	Exon 3 of 5	5	NM_020426.4	ENSP00000483897.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	15
DANN	Benign	0.79
DEOGEN2	Benign	0.0022	T;T
Eigen	Benign	-0.92
Eigen_PC	Benign	-0.99
FATHMM_MKL	Benign	0.024	N
LIST_S2	Benign	0.63	.;T
M_CAP	Benign	0.0035	T
MetaRNN	Benign	0.070	T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	1.7	L;L
PhyloP100		1.2
PrimateAI	Benign	0.45	T
Sift4G	Benign	0.58	T;T
Polyphen		0.24	B;B
Vest4		0.18
MutPred		0.38		Gain of disorder (P = 0.0225);Gain of disorder (P = 0.0225);
MVP		0.061
ClinPred		0.42	T
GERP RS		-0.34
Varity_R		0.16
gMVP		0.64

Splicing

Name	Calibrated prediction	Score	Prediction
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: rs780416398; hg19: chr17-34264863;