1-232809509-C-G

Position:

• chr1-232809509-C-G

Variant summary

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

The NM_019090.3(MAP10):​c.*1342C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0934 in 151,904 control chromosomes in the GnomAD database, including 1,035 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 0.093 (1035 hom., cov: 32)
• Consequence: MAP10 NM_019090.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

MAP10 (HGNC:29265): (microtubule associated protein 10) Enables microtubule binding activity. Involved in microtubule cytoskeleton organization; positive regulation of cytokinesis; and regulation of microtubule-based process. Located in microtubule cytoskeleton and midbody. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP10	NM_019090.3	c.*1342C>G		3_prime_UTR_variant	1/1	ENST00000418460.4	NP_061963.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP10	ENST00000418460.4	c.*1342C>G		3_prime_UTR_variant	1/1	6	NM_019090.3	ENSP00000403208.2

Frequencies

GnomAD3 genomes AF: 0.0932 AC: 14143 AN: 151786 Hom.: 1027 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.0603

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0430

Gnomad OTH AF: 0.0923

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0934 AC: 14186 AN: 151904 Hom.: 1035 Cov.: 32 AF XY: 0.0915 AC XY: 6788 AN XY: 74224

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0742

Gnomad4 ASJ AF: 0.0603

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0835

Gnomad4 FIN AF: 0.0191

Gnomad4 NFE AF: 0.0430

Gnomad4 OTH AF: 0.0947

Alfa AF: 0.0164 Hom.: 11

Bravo AF: 0.103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.0
DANN	Benign	0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10489578; hg19: chr1-232945255;