NM_001139442.2:c.1840+12080C>T

Variant names:

• chr9-121848257-G-A
• rs10760198
• NM_001139442.2:c.1840+12080C>T

Variant summary

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

The NM_001139442.2(TTLL11):​c.1840+12080C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 151,654 control chromosomes in the GnomAD database, including 24,449 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 0.56 (24449 hom., cov: 31)
• Consequence: TTLL11 NM_001139442.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 2 publications found

Genes affected

TTLL11 (HGNC:18113): (tubulin tyrosine ligase like 11) Predicted to enable tubulin binding activity and tubulin-glutamic acid ligase activity. Predicted to be involved in microtubule cytoskeleton organization and protein polyglutamylation. Predicted to act upstream of or within microtubule severing. Predicted to be located in cytosol. Predicted to be active in cilium. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000298078 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001139442.2. 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
	TTLL11	NM_001139442.2	MANE Select	c.1840+12080C>T		intron	N/A	NP_001132914.2
	TTLL11	NM_001386833.1		c.187+12080C>T		intron	N/A	NP_001373762.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTLL11	ENST00000321582.11	TSL:5 MANE Select	c.1840+12080C>T		intron	N/A	ENSP00000321346.6
	TTLL11	ENST00000373778.5	TSL:5	n.*918+12080C>T		intron	N/A	ENSP00000478392.1
	TTLL11	ENST00000474723.5	TSL:2	n.*1114+12080C>T		intron	N/A	ENSP00000479407.1

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85336 AN: 151542 Hom.: 24429 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.563 AC: 85401 AN: 151654 Hom.: 24449 Cov.: 31 AF XY: 0.567 AC XY: 42023 AN XY: 74100

African (AFR) AF: 0.481 AC: 19852 AN: 41282

American (AMR) AF: 0.473 AC: 7209 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2100 AN: 3468

East Asian (EAS) AF: 0.767 AC: 3964 AN: 5170

South Asian (SAS) AF: 0.689 AC: 3303 AN: 4796

European-Finnish (FIN) AF: 0.650 AC: 6791 AN: 10446

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40381 AN: 67934

Other (OTH) AF: 0.537 AC: 1134 AN: 2112

Alfa AF: 0.577 Hom.: 5734

Bravo AF: 0.542

Asia WGS AF: 0.725 AC: 2525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.72
PhyloP100		-1.7
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: rs10760198; hg19: chr9-124610536;