1-232808823-C-T

Position:

• chr1-232808823-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP10	NM_019090.3	c.*656C>T		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.*656C>T		3_prime_UTR_variant	1/1	6	NM_019090.3	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

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.594

Alfa AF: 0.660 Hom.: 38811

Bravo AF: 0.546

Asia WGS AF: 0.658 AC: 2286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

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