rs16843614

Variant names:

• chr2-209730600-G-A
• rs16843614
• NM_001375505.1:c.*203G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MAP2	NM_001375505.1	c.*203G>A		3_prime_UTR_variant	Exon 16 of 16	ENST00000682079.1	NP_001362434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP2	ENST00000682079.1	c.*203G>A		3_prime_UTR_variant	Exon 16 of 16		NM_001375505.1	ENSP00000507035.1

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

African (AFR) AF: 0.218 AC: 2561 AN: 11746

American (AMR) AF: 0.0717 AC: 1257 AN: 17540

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 1281 AN: 12628

East Asian (EAS) AF: 0.224 AC: 6308 AN: 28118

South Asian (SAS) AF: 0.144 AC: 6045 AN: 42124

European-Finnish (FIN) AF: 0.0817 AC: 2141 AN: 26208

Middle Eastern (MID) AF: 0.119 AC: 213 AN: 1792

European-Non Finnish (NFE) AF: 0.0674 AC: 16885 AN: 250510

Other (OTH) AF: 0.0947 AC: 2287 AN: 24150

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

African (AFR) AF: 0.211 AC: 8729 AN: 41464

American (AMR) AF: 0.0825 AC: 1262 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1166 AN: 5170

South Asian (SAS) AF: 0.150 AC: 725 AN: 4818

European-Finnish (FIN) AF: 0.0805 AC: 853 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0689 AC: 4688 AN: 68008

Other (OTH) AF: 0.105 AC: 223 AN: 2116

Alfa AF: 0.0825 Hom.: 885

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
PhyloP100		3.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16843614; hg19: chr2-210595324;