2-210458673-C-T

Variant names:

• chr2-210458673-C-T
• rs725379
• NM_006055.3:c.200-3359G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006055.3(LANCL1):​c.200-3359G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 151,994 control chromosomes in the GnomAD database, including 31,151 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 0.63 (31151 hom., cov: 31)
• Consequence: LANCL1 NM_006055.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.795
• Publications: 2 publications found

Genes affected

LANCL1 (HGNC:6508): (LanC like glutathione S-transferase 1) This gene encodes a loosely associated peripheral membrane protein related to the LanC family of bacterial membrane-associated proteins involved in the biosynthesis of antimicrobial peptides. This protein may play a role as a peptide-modifying enzyme component in eukaryotic cells. Previously considered a member of the G-protein-coupled receptor superfamily, this protein is now in the LanC family. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Nov 2008]

LANCL1-AS1 (HGNC:50727): (LANCL1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LANCL1	NM_006055.3	c.200-3359G>A		intron_variant	Intron 3 of 9	ENST00000450366.7	NP_006046.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LANCL1	ENST00000450366.7	c.200-3359G>A		intron_variant	Intron 3 of 9	1	NM_006055.3	ENSP00000393597.2

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95884 AN: 151876 Hom.: 31122 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.631 AC: 95966 AN: 151994 Hom.: 31151 Cov.: 31 AF XY: 0.633 AC XY: 46990 AN XY: 74278

African (AFR) AF: 0.751 AC: 31141 AN: 41478

American (AMR) AF: 0.662 AC: 10122 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1690 AN: 3470

East Asian (EAS) AF: 0.822 AC: 4233 AN: 5150

South Asian (SAS) AF: 0.632 AC: 3039 AN: 4808

European-Finnish (FIN) AF: 0.565 AC: 5962 AN: 10550

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37838 AN: 67932

Other (OTH) AF: 0.597 AC: 1263 AN: 2114

Alfa AF: 0.620 Hom.: 3990

Bravo AF: 0.648

Asia WGS AF: 0.751 AC: 2611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.45
PhyloP100		0.80
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs725379; hg19: chr2-211323397;