chr1-1186414-G-A

Position:

• chr1-1186414-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TTLL10	NM_001130045.2	c.1401+1305G>A		intron_variant		ENST00000379289.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTLL10	ENST00000379289.6	c.1401+1305G>A		intron_variant		2	NM_001130045.2	P1
TTLL10	ENST00000379290.6	c.1401+1305G>A		intron_variant		1		P1
TTLL10	ENST00000486379.1	c.74+1305G>A		intron_variant, NMD_transcript_variant		3

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

Gnomad4 AFR AF: 0.0460

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.0991

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.154

Alfa AF: 0.131 Hom.: 2337

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs11260549; hg19: chr1-1121794;