NM_022818.5:c.204-66T>C

Variant names:

• chr16-87402857-T-C
• rs8051218
• NM_022818.5:c.204-66T>C

Variant summary

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

The NM_022818.5(MAP1LC3B):​c.204-66T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.08 in 1,586,986 control chromosomes in the GnomAD database, including 13,961 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 0.19 (6186 hom., cov: 33)
  • Exomes 𝑓: 0.068 (7775 hom.)
• Consequence: MAP1LC3B NM_022818.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 10 publications found

Genes affected

MAP1LC3B (HGNC:13352): (microtubule associated protein 1 light chain 3 beta) The product of this gene is a subunit of neuronal microtubule-associated MAP1A and MAP1B proteins, which are involved in microtubule assembly and important for neurogenesis. Studies on the rat homolog implicate a role for this gene in autophagy, a process that involves the bulk degradation of cytoplasmic component. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022818.5. 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
	MAP1LC3B	NM_022818.5	MANE Select	c.204-66T>C		intron	N/A	NP_073729.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP1LC3B	ENST00000268607.10	TSL:1 MANE Select	c.204-66T>C		intron	N/A	ENSP00000268607.5
	MAP1LC3B	ENST00000564844.1	TSL:1	n.*938-66T>C		intron	N/A	ENSP00000454293.1
	MAP1LC3B	ENST00000570189.5	TSL:1	n.*149-66T>C		intron	N/A	ENSP00000457141.1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28848 AN: 152120 Hom.: 6166 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0345

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.173

GnomAD4 exome AF: 0.0684 AC: 98067 AN: 1434748 Hom.: 7775 AF XY: 0.0664 AC XY: 47341 AN XY: 713036

African (AFR) AF: 0.545 AC: 17887 AN: 32796

American (AMR) AF: 0.0688 AC: 2893 AN: 42032

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 3144 AN: 25540

East Asian (EAS) AF: 0.000102 AC: 4 AN: 39378

South Asian (SAS) AF: 0.0343 AC: 2887 AN: 84086

European-Finnish (FIN) AF: 0.0289 AC: 1527 AN: 52918

Middle Eastern (MID) AF: 0.153 AC: 866 AN: 5674

European-Non Finnish (NFE) AF: 0.0580 AC: 63442 AN: 1092940

Other (OTH) AF: 0.0912 AC: 5417 AN: 59384

GnomAD4 genome AF: 0.190 AC: 28912 AN: 152238 Hom.: 6186 Cov.: 33 AF XY: 0.183 AC XY: 13616 AN XY: 74458

African (AFR) AF: 0.528 AC: 21913 AN: 41474

American (AMR) AF: 0.0988 AC: 1511 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0348 AC: 168 AN: 4830

European-Finnish (FIN) AF: 0.0267 AC: 284 AN: 10632

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.0604 AC: 4110 AN: 68028

Other (OTH) AF: 0.171 AC: 361 AN: 2116

Alfa AF: 0.141 Hom.: 3587

Bravo AF: 0.212

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.81
DANN	Benign	0.35
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

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: rs8051218; hg19: chr16-87436463;