NM_001130045.2:c.1401+1305G>A

Variant names:

• chr1-1186414-G-A
• rs11260549
• NM_001130045.2:c.1401+1305G>A

Variant summary

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

The NM_001130045.2(TTLL10):​c.1401+1305G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,136 control chromosomes in the GnomAD database, including 2,561 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 0.14 (2561 hom., cov: 32)
• Consequence: TTLL10 NM_001130045.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93
• Publications: 8 publications found

Genes affected

TTLL10 (HGNC:26693): (tubulin tyrosine ligase like 10) Predicted to enable protein-glycine ligase activity, elongating. Predicted to be involved in protein polyglycylation. Predicted to be located in axoneme and microtubule cytoskeleton. [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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTLL10	NM_001130045.2	c.1401+1305G>A		intron_variant	Intron 13 of 15	ENST00000379289.6	NP_001123517.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTLL10	ENST00000379289.6	c.1401+1305G>A		intron_variant	Intron 13 of 15	2	NM_001130045.2	ENSP00000368591.1
TTLL10	ENST00000379290.6	c.1401+1305G>A		intron_variant	Intron 13 of 15	1		ENSP00000368592.1
TTLL10	ENST00000486379.1	n.72+1305G>A		intron_variant	Intron 1 of 4	3		ENSP00000464269.1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21058 AN: 152018 Hom.: 2559 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.139 AC: 21082 AN: 152136 Hom.: 2561 Cov.: 32 AF XY: 0.145 AC XY: 10762 AN XY: 74366

African (AFR) AF: 0.0460 AC: 1908 AN: 41510

American (AMR) AF: 0.306 AC: 4685 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 344 AN: 3472

East Asian (EAS) AF: 0.573 AC: 2970 AN: 5180

South Asian (SAS) AF: 0.264 AC: 1269 AN: 4810

European-Finnish (FIN) AF: 0.108 AC: 1141 AN: 10572

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8287 AN: 67978

Other (OTH) AF: 0.154 AC: 325 AN: 2112

Alfa AF: 0.128 Hom.: 3641

Bravo AF: 0.148

Asia WGS AF: 0.394 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.55
PhyloP100		-2.9
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: rs11260549; hg19: chr1-1121794;