chr2-209730600-G-A

Position:

• chr2-209730600-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001375505.1(MAP2):​c.*203G>A variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.101 in 566,952 control chromosomes in the GnomAD database, including 3,845 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 0.12 (1398 hom., cov: 32)
  • Exomes 𝑓: 0.094 (2447 hom.)
• Consequence: MAP2 NM_001375505.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.94

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP2	NM_001375505.1	c.*203G>A		3_prime_UTR_variant	16/16	ENST00000682079.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP2	ENST00000682079.1	c.*203G>A		3_prime_UTR_variant	16/16		NM_001375505.1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18086 AN: 152018 Hom.: 1395 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0805

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.106

GnomAD4 exome AF: 0.0940 AC: 38978 AN: 414816 Hom.: 2447 Cov.: 4 AF XY: 0.0957 AC XY: 20903 AN XY: 218330

Gnomad4 AFR exome AF: 0.218

Gnomad4 AMR exome AF: 0.0717

Gnomad4 ASJ exome AF: 0.101

Gnomad4 EAS exome AF: 0.224

Gnomad4 SAS exome AF: 0.144

Gnomad4 FIN exome AF: 0.0817

Gnomad4 NFE exome AF: 0.0674

Gnomad4 OTH exome AF: 0.0947

GnomAD4 genome AF: 0.119 AC: 18109 AN: 152136 Hom.: 1398 Cov.: 32 AF XY: 0.120 AC XY: 8940 AN XY: 74388

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.0825

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0805

Gnomad4 NFE AF: 0.0689

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0782 Hom.: 572

Bravo AF: 0.121

Asia WGS AF: 0.180 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	13
DANN	Benign	0.86

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: rs16843614; hg19: chr2-210595324;