rs8181728

chr12-116562092-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001085481.3(MAP1LC3B2):c.-102+2659G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,030 control chromosomes in the GnomAD database, including 6,795 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 0.29 (6795 hom., cov: 32)
• Consequence: MAP1LC3B2 NM_001085481.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

Genes affected

MAP1LC3B2 (HGNC:34390): (microtubule associated protein 1 light chain 3 beta 2) Predicted to enable microtubule binding activity and ubiquitin protein ligase binding activity. Predicted to be involved in autophagy of mitochondrion; cellular response to nitrogen starvation; and macroautophagy. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP1LC3B2	NM_001085481.3	c.-102+2659G>A		intron_variant		ENST00000556529.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP1LC3B2	ENST00000556529.4	c.-102+2659G>A		intron_variant		3	NM_001085481.3	P1

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43664 AN: 151912 Hom.: 6785 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.287 AC: 43700 AN: 152030 Hom.: 6795 Cov.: 32 AF XY: 0.287 AC XY: 21289 AN XY: 74298

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.243

Alfa AF: 0.248 Hom.: 841

Bravo AF: 0.283

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.30
Dann	Benign	0.59

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: rs8181728; hg19: chr12-116999897;