chr2-209731096-G-C

Variant names:

• chr2-209731096-G-C
• rs16843618
• NM_001375505.1:c.*699G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001375505.1(MAP2):​c.*699G>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.119 in 152,486 control chromosomes in the GnomAD database, including 1,401 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: 0.089 (3 hom.)
• Consequence: MAP2 NM_001375505.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.23
• Publications: 6 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=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP2	NM_001375505.1	c.*699G>C		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.*699G>C		3_prime_UTR_variant	Exon 16 of 16		NM_001375505.1	ENSP00000507035.1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18091 AN: 151894 Hom.: 1395 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0811

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.105

GnomAD4 exome AF: 0.0886 AC: 42 AN: 474 Hom.: 3 Cov.: 0 AF XY: 0.0972 AC XY: 28 AN XY: 288

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0892 AC: 38 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0750 AC: 3 AN: 40

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.119 AC: 18114 AN: 152012 Hom.: 1398 Cov.: 32 AF XY: 0.120 AC XY: 8942 AN XY: 74322

African (AFR) AF: 0.211 AC: 8735 AN: 41426

American (AMR) AF: 0.0827 AC: 1261 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3472

East Asian (EAS) AF: 0.225 AC: 1163 AN: 5168

South Asian (SAS) AF: 0.151 AC: 728 AN: 4816

European-Finnish (FIN) AF: 0.0811 AC: 857 AN: 10570

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

European-Non Finnish (NFE) AF: 0.0689 AC: 4685 AN: 67986

Other (OTH) AF: 0.105 AC: 221 AN: 2112

Alfa AF: 0.0990 Hom.: 141

Bravo AF: 0.121

Asia WGS AF: 0.180 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	15
DANN	Benign	0.88
PhyloP100		5.2
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: rs16843618; hg19: chr2-210595820;