rs781894430

Variant names:

• chrX-37572160-A-C
• rs781894430
• NM_001170331.2:c.290A>C

Your query was ambiguous. Multiple possible variants found:

• chrX-37572160-A-C
• chrX-37572160-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001170331.2(LANCL3):​c.290A>C​(p.Lys97Thr) 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. 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. K97M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 23)
• Consequence: LANCL3 NM_001170331.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.40

Genes affected

LANCL3 (HGNC:24767): (LanC like family member 3) Predicted to be involved in carbohydrate metabolic process. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000250349 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.21116999).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LANCL3	NM_001170331.2	c.290A>C	p.Lys97Thr	missense_variant	Exon 1 of 5	ENST00000378619.4	NP_001163802.1
LANCL3	NM_198511.3	c.290A>C	p.Lys97Thr	missense_variant	Exon 1 of 6		NP_940913.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LANCL3	ENST00000378619.4	c.290A>C	p.Lys97Thr	missense_variant	Exon 1 of 5	1	NM_001170331.2	ENSP00000367882.4
LANCL3	ENST00000378621.7	c.290A>C	p.Lys97Thr	missense_variant	Exon 1 of 6	1		ENSP00000367885.3
ENSG00000250349	ENST00000465127.1	c.171+146160A>C		intron_variant	Intron 3 of 8	5		ENSP00000417050.1
LANCL3	ENST00000614025.4	c.290A>C	p.Lys97Thr	missense_variant	Exon 1 of 5	2		ENSP00000479231.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 23

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Uncertain	0.98
DEOGEN2	Benign	0.037	.;.;T
FATHMM_MKL	Benign	0.73	D
LIST_S2	Benign	0.67	T;.;T
M_CAP	Pathogenic	0.33	D
MetaRNN	Benign	0.21	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.94	L;L;L
PrimateAI	Pathogenic	0.96	D
PROVEAN	Benign	-1.8	.;N;N
REVEL	Benign	0.12
Sift	Benign	0.37	.;T;T
Sift4G	Benign	0.19	T;T;T
Polyphen		0.037	B;B;B
Vest4		0.21
MutPred		0.57		Gain of phosphorylation at K97 (P = 0.0587);Gain of phosphorylation at K97 (P = 0.0587);Gain of phosphorylation at K97 (P = 0.0587);
MVP		0.19
MPC		0.58
ClinPred		0.31	T
GERP RS		4.6
Varity_R		0.089
gMVP		0.45

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: rs781894430; hg19: chrX-37431413;