rs11167239

Variant names:

• chr20-34552668-G-A
• rs11167239
• NM_181509.3:c.52+2639G>A

Variant summary

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

The NM_181509.3(MAP1LC3A):​c.52+2639G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,198 control chromosomes in the GnomAD database, including 14,756 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 0.43 (14756 hom., cov: 34)
• Consequence: MAP1LC3A NM_181509.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 5 publications found

Genes affected

MAP1LC3A (HGNC:6838): (microtubule associated protein 1 light chain 3 alpha) MAP1A and MAP1B are microtubule-associated proteins which mediate the physical interactions between microtubules and components of the cytoskeleton. MAP1A and MAP1B each consist of a heavy chain subunit and multiple light chain subunits. The protein encoded by this gene is one of the light chain subunits and can associate with either MAP1A or MAP1B. Two transcript variants encoding different isoforms have been found for this gene. The expression of variant 1 is suppressed in many tumor cell lines, suggesting that may be involved in carcinogenesis. [provided by RefSeq, Feb 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP1LC3A	NM_181509.3	c.52+2639G>A		intron_variant	Intron 2 of 4		NP_852610.1
MAP1LC3A	XM_011529084.3	c.52+2639G>A		intron_variant	Intron 2 of 7		XP_011527386.1
MAP1LC3A	XM_011529085.3	c.52+2639G>A		intron_variant	Intron 2 of 5		XP_011527387.1
MAP1LC3A	XM_047440559.1	c.-132+5752G>A		intron_variant	Intron 1 of 4		XP_047296515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP1LC3A	ENST00000374837.7	c.52+2639G>A		intron_variant	Intron 2 of 4	3		ENSP00000363970.3

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65623 AN: 152080 Hom.: 14760 Cov.: 34

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.431 AC: 65632 AN: 152198 Hom.: 14756 Cov.: 34 AF XY: 0.431 AC XY: 32100 AN XY: 74410

African (AFR) AF: 0.317 AC: 13165 AN: 41534

American (AMR) AF: 0.361 AC: 5517 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2025 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2043 AN: 5172

South Asian (SAS) AF: 0.411 AC: 1985 AN: 4830

European-Finnish (FIN) AF: 0.529 AC: 5605 AN: 10604

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33776 AN: 67972

Other (OTH) AF: 0.441 AC: 932 AN: 2112

Alfa AF: 0.466 Hom.: 7889

Bravo AF: 0.415

Asia WGS AF: 0.400 AC: 1392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.47
DANN	Benign	0.43
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11167239; hg19: chr20-33140472;