rs1949041

chr2-209643477-A-Cchr2-209643477-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375505.1(MAP2):c.-29-9665A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 152,248 control chromosomes in the GnomAD database, including 813 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 0.067 (813 hom., cov: 32)
• Consequence: MAP2 NM_001375505.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73

Genes affected

MAP2 (HGNC:6839): (microtubule associated protein 2) This gene encodes a protein that belongs to the microtubule-associated protein family. The proteins of this family are thought to be involved in microtubule assembly, which is an essential step in neurogenesis. The products of similar genes in rat and mouse are neuron-specific cytoskeletal proteins that are enriched in dentrites, implicating a role in determining and stabilizing dentritic shape during neuron development. A number of alternatively spliced variants encoding distinct isoforms have been described. [provided by RefSeq, Jan 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP2	NM_001375505.1	c.-29-9665A>C		intron_variant		ENST00000682079.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP2	ENST00000682079.1	c.-29-9665A>C		intron_variant			NM_001375505.1

Frequencies

GnomAD3 genomes AF: 0.0666 AC: 10136 AN: 152130 Hom.: 807 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00288

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.00895

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0124

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0668 AC: 10167 AN: 152248 Hom.: 813 Cov.: 32 AF XY: 0.0688 AC XY: 5124 AN XY: 74460

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.00895

Gnomad4 NFE AF: 0.0124

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.00517 Hom.: 2

Bravo AF: 0.0678

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	12
Dann	Benign	0.85

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: rs1949041; hg19: chr2-210508201;