rs1531312

Variant names:

• chr5-72115891-T-C
• rs1531312
• NM_005909.5:c.286+92T>C

Variant summary

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

The NM_005909.5(MAP1B):​c.286+92T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 839,288 control chromosomes in the GnomAD database, including 194,516 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 0.64 (32223 hom., cov: 32)
  • Exomes 𝑓: 0.68 (162293 hom.)
• Consequence: MAP1B NM_005909.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

Genes affected

MAP1B (HGNC:6836): (microtubule associated protein 1B) 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 product of this gene is a precursor polypeptide that presumably undergoes proteolytic processing to generate the final MAP1B heavy chain and LC1 light chain. Gene knockout studies of the mouse microtubule-associated protein 1B gene suggested an important role in development and function of the nervous system. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP1B	NM_005909.5	c.286+92T>C		intron_variant	Intron 2 of 6	ENST00000296755.12	NP_005900.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP1B	ENST00000296755.12	c.286+92T>C		intron_variant	Intron 2 of 6	1	NM_005909.5	ENSP00000296755.7

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97806 AN: 151904 Hom.: 32205 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.676

GnomAD4 exome AF: 0.680 AC: 467489 AN: 687266 Hom.: 162293 Cov.: 9 AF XY: 0.683 AC XY: 251082 AN XY: 367564

Gnomad4 AFR exome AF: 0.541

Gnomad4 AMR exome AF: 0.597

Gnomad4 ASJ exome AF: 0.769

Gnomad4 EAS exome AF: 0.341

Gnomad4 SAS exome AF: 0.659

Gnomad4 FIN exome AF: 0.737

Gnomad4 NFE exome AF: 0.714

Gnomad4 OTH exome AF: 0.682

GnomAD4 genome AF: 0.644 AC: 97878 AN: 152022 Hom.: 32223 Cov.: 32 AF XY: 0.641 AC XY: 47630 AN XY: 74292

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.674

Alfa AF: 0.702 Hom.: 77128

Bravo AF: 0.631

Asia WGS AF: 0.531 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.4
DANN	Benign	0.87

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: rs1531312; hg19: chr5-71411718; COSMIC: COSV57095796;