1-232808823-C-T

Variant names:

• chr1-232808823-C-T
• rs1845789
• NM_019090.3:c.*656C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019090.3(MAP10):​c.*656C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,968 control chromosomes in the GnomAD database, including 28,573 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 0.57 (28573 hom., cov: 33)
• Consequence: MAP10 NM_019090.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019090.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP10	NM_019090.3	MANE Select	c.*656C>T		3_prime_UTR	Exon 1 of 1	NP_061963.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP10	ENST00000418460.4	TSL:6 MANE Select	c.*656C>T		3_prime_UTR	Exon 1 of 1	ENSP00000403208.2

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87274 AN: 151848 Hom.: 28560 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.574 AC: 87299 AN: 151968 Hom.: 28573 Cov.: 33 AF XY: 0.585 AC XY: 43466 AN XY: 74282

African (AFR) AF: 0.231 AC: 9570 AN: 41448

American (AMR) AF: 0.652 AC: 9956 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2354 AN: 3468

East Asian (EAS) AF: 0.652 AC: 3370 AN: 5170

South Asian (SAS) AF: 0.735 AC: 3546 AN: 4822

European-Finnish (FIN) AF: 0.788 AC: 8343 AN: 10594

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.709 AC: 48156 AN: 67880

Other (OTH) AF: 0.594 AC: 1252 AN: 2108

Alfa AF: 0.653 Hom.: 52066

Bravo AF: 0.546

Asia WGS AF: 0.658 AC: 2286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.79
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1845789; hg19: chr1-232944569; COSMIC: COSV69363457;