rs2089222

Variant names:

• chr12-116564853-G-A
• rs2089222
• NM_001085481.3:c.-102+5420G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-116564853-G-A
• chr12-116564853-G-C
• chr12-116564853-G-T

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+5420G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,200 control chromosomes in the GnomAD database, including 2,067 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 0.12 (2067 hom., cov: 32)
• Consequence: MAP1LC3B2 NM_001085481.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 16 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP1LC3B2	NM_001085481.3	c.-102+5420G>A		intron_variant	Intron 1 of 1	ENST00000556529.4	NP_001078950.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP1LC3B2	ENST00000556529.4	c.-102+5420G>A		intron_variant	Intron 1 of 1	3	NM_001085481.3	ENSP00000450524.1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18142 AN: 152082 Hom.: 2060 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0285

Gnomad FIN AF: 0.0325

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0339

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.119 AC: 18171 AN: 152200 Hom.: 2067 Cov.: 32 AF XY: 0.121 AC XY: 9005 AN XY: 74436

African (AFR) AF: 0.234 AC: 9708 AN: 41502

American (AMR) AF: 0.282 AC: 4312 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1011 AN: 5182

South Asian (SAS) AF: 0.0280 AC: 135 AN: 4830

European-Finnish (FIN) AF: 0.0325 AC: 345 AN: 10608

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0339 AC: 2308 AN: 68020

Other (OTH) AF: 0.114 AC: 241 AN: 2110

Alfa AF: 0.0667 Hom.: 3092

Bravo AF: 0.150

Asia WGS AF: 0.116 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.18
PhyloP100		-0.40

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: rs2089222; hg19: chr12-117002658;