rs10517618

Variant names:

• chr4-155349603-A-C
• rs10517618
• NM_001039580.2:c.1822-1698T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-155349603-A-C
• chr4-155349603-A-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MAP9	NM_001039580.2	c.1822-1698T>G		intron_variant	Intron 13 of 13	ENST00000311277.9	NP_001034669.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP9	ENST00000311277.9	c.1822-1698T>G		intron_variant	Intron 13 of 13	1	NM_001039580.2	ENSP00000310593.4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.357 AC: 5 AN: 14

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.728 AC: 30184 AN: 41464

American (AMR) AF: 0.543 AC: 8277 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1638 AN: 3468

East Asian (EAS) AF: 0.792 AC: 4101 AN: 5176

South Asian (SAS) AF: 0.521 AC: 2511 AN: 4816

European-Finnish (FIN) AF: 0.713 AC: 7525 AN: 10558

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36855 AN: 67978

Other (OTH) AF: 0.570 AC: 1200 AN: 2106

Alfa AF: 0.595 Hom.: 3539

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
PhyloP100		-0.056
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: rs10517618; hg19: chr4-156270755;