2-210458673-C-T

Position:

• chr2-210458673-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LANCL1	NM_006055.3	c.200-3359G>A		intron_variant		ENST00000450366.7
LANCL1-AS1	NR_110604.1	n.369-1802C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LANCL1	ENST00000450366.7	c.200-3359G>A		intron_variant		1	NM_006055.3	P1
LANCL1-AS1	ENST00000420418.5	n.315-1802C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.597

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

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: rs725379; hg19: chr2-211323397;