rs10517618

chr4-155349603-A-Cchr4-155349603-A-G

Variant summary

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

The NM_001039580.2(MAP9):c.1822-1698T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,044 control chromosomes in the GnomAD database, including 29,228 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 0.61 (29227 hom., cov: 32)
  • Exomes 𝑓: 0.38 (1 hom.)
• Consequence: MAP9 NM_001039580.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

Genes affected

MAP9 (HGNC:26118): (microtubule associated protein 9) ASAP is a microtubule-associated protein required for spindle function, mitotic progression, and cytokinesis (Saffin et al., 2005 [PubMed 16049101]).[supplied by OMIM, Mar 2008]

MAP9-AS1 (HGNC:56110): (MAP9 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP9	NM_001039580.2	c.1822-1698T>G		intron_variant		ENST00000311277.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP9	ENST00000311277.9	c.1822-1698T>G		intron_variant		1	NM_001039580.2	P1
MAP9-AS1	ENST00000630664.2	n.209-4606A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92945 AN: 151912 Hom.: 29178 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.566

GnomAD4 exome AF: 0.375 AC: 6 AN: 16 Hom.: 1 Cov.: 0 AF XY: 0.429 AC XY: 6 AN XY: 14

Gnomad4 EAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.357

GnomAD4 genome AF: 0.612 AC: 93052 AN: 152028 Hom.: 29227 Cov.: 32 AF XY: 0.619 AC XY: 45958 AN XY: 74282

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.570

Alfa AF: 0.589 Hom.: 3325

Bravo AF: 0.603

Asia WGS AF: 0.685 AC: 2380 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.5
Dann	Benign	0.70

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: rs10517618; hg19: chr4-156270755;