16-87402857-T-C

Position:

• chr16-87402857-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP1LC3B	NM_022818.5	c.204-66T>C		intron_variant		ENST00000268607.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP1LC3B	ENST00000268607.10	c.204-66T>C		intron_variant		1	NM_022818.5	P1
MAP1LC3B	ENST00000564844.1	c.*938-66T>C		intron_variant, NMD_transcript_variant		1
MAP1LC3B	ENST00000570189.5	c.*149-66T>C		intron_variant, NMD_transcript_variant		1
MAP1LC3B	ENST00000650688.1	c.204-66T>C		intron_variant				P1

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

Gnomad4 AFR exome AF: 0.545

Gnomad4 AMR exome AF: 0.0688

Gnomad4 ASJ exome AF: 0.123

Gnomad4 EAS exome AF: 0.000102

Gnomad4 SAS exome AF: 0.0343

Gnomad4 FIN exome AF: 0.0289

Gnomad4 NFE exome AF: 0.0580

Gnomad4 OTH exome AF: 0.0912

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

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.0988

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0348

Gnomad4 FIN AF: 0.0267

Gnomad4 NFE AF: 0.0604

Gnomad4 OTH AF: 0.171

Alfa AF: 0.0762 Hom.: 612

Bravo AF: 0.212

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.81
DANN	Benign	0.35

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: rs8051218; hg19: chr16-87436463;