chr12-116562092-G-A

Variant names:

• chr12-116562092-G-A
• rs8181728
• NM_001085481.3:c.-102+2659G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001085481.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP1LC3B2	NM_001085481.3	MANE Select	c.-102+2659G>A		intron	N/A	NP_001078950.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP1LC3B2	ENST00000556529.4	TSL:3 MANE Select	c.-102+2659G>A		intron	N/A	ENSP00000450524.1

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

African (AFR) AF: 0.378 AC: 15684 AN: 41474

American (AMR) AF: 0.198 AC: 3025 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3464

East Asian (EAS) AF: 0.321 AC: 1652 AN: 5152

South Asian (SAS) AF: 0.343 AC: 1652 AN: 4822

European-Finnish (FIN) AF: 0.321 AC: 3384 AN: 10546

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16718 AN: 67970

Other (OTH) AF: 0.243 AC: 514 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.59
PhyloP100		-1.9

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: rs8181728; hg19: chr12-116999897;