7-55388713-C-G

Variant names:

• chr7-55388713-C-G
• rs7796351
• NM_018697.4:c.205-3080C>G

Variant summary

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

The NM_018697.4(LANCL2):​c.205-3080C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,114 control chromosomes in the GnomAD database, including 10,430 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 0.36 (10430 hom., cov: 32)
• Consequence: LANCL2 NM_018697.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• Publications: 1 publications found

Genes affected

LANCL2 (HGNC:6509): (LanC like glutathione S-transferase 2) Enables phosphatidylinositol-3-phosphate binding activity; phosphatidylinositol-4-phosphate binding activity; and phosphatidylinositol-5-phosphate binding activity. Involved in negative regulation of transcription, DNA-templated and positive regulation of abscisic acid-activated signaling pathway. Located in several cellular components, including cortical actin cytoskeleton; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LANCL2	NM_018697.4	c.205-3080C>G		intron_variant	Intron 1 of 8	ENST00000254770.3	NP_061167.1
LANCL2	XM_047420614.1	c.-57-3080C>G		intron_variant	Intron 2 of 9		XP_047276570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LANCL2	ENST00000254770.3	c.205-3080C>G		intron_variant	Intron 1 of 8	1	NM_018697.4	ENSP00000254770.2
LANCL2	ENST00000452107.6	n.*185-3080C>G		intron_variant	Intron 2 of 9	5		ENSP00000387598.2

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54831 AN: 151996 Hom.: 10410 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.361 AC: 54890 AN: 152114 Hom.: 10430 Cov.: 32 AF XY: 0.364 AC XY: 27088 AN XY: 74360

African (AFR) AF: 0.328 AC: 13609 AN: 41488

American (AMR) AF: 0.511 AC: 7823 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1681 AN: 3468

East Asian (EAS) AF: 0.549 AC: 2831 AN: 5156

South Asian (SAS) AF: 0.348 AC: 1676 AN: 4812

European-Finnish (FIN) AF: 0.296 AC: 3141 AN: 10606

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 23009 AN: 67974

Other (OTH) AF: 0.362 AC: 764 AN: 2110

Alfa AF: 0.208 Hom.: 463

Bravo AF: 0.379

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.6
DANN	Benign	0.44
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.13		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: rs7796351; hg19: chr7-55456406;