rs9288410

Positions:

• chr2-209633537-G-A
• chr2-209633537-G-C

Variant summary

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

The NM_001375505.1(MAP2):​c.-30+8408G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,044 control chromosomes in the GnomAD database, including 11,160 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 0.30 (11160 hom., cov: 32)
• Consequence: MAP2 NM_001375505.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP2	NM_001375505.1	c.-30+8408G>A		intron_variant		ENST00000682079.1	NP_001362434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP2	ENST00000682079.1	c.-30+8408G>A		intron_variant			NM_001375505.1	ENSP00000507035

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45301 AN: 151926 Hom.: 11131 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.298 AC: 45371 AN: 152044 Hom.: 11160 Cov.: 32 AF XY: 0.299 AC XY: 22248 AN XY: 74332

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.268

Alfa AF: 0.232 Hom.: 1163

Bravo AF: 0.313

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.46

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: rs9288410; hg19: chr2-210498261;