rs7219021

Variant names:

• chr17-48763179-T-C
• rs7219021
• NM_001130918.3:c.*1-206A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-48763179-T-C
• chr17-48763179-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001130918.3(TTLL6):​c.*1-206A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: TTLL6 NM_001130918.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.828
• Publications: 11 publications found

Genes affected

TTLL6 (HGNC:26664): (tubulin tyrosine ligase like 6) 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 bundle formation; microtubule severing; and positive regulation of cilium movement. Located in ciliary basal body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130918.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTLL6	NM_001130918.3	MANE Select	c.*1-206A>G		intron	N/A	NP_001124390.1	Q8N841-1
	TTLL6	NM_173623.4		c.*1-206A>G		intron	N/A	NP_775894.2	A0AAA9X7X9
	TTLL6	NM_001366314.2		c.1582-206A>G		intron	N/A	NP_001353243.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTLL6	ENST00000393382.8	TSL:2 MANE Select	c.*1-206A>G		intron	N/A	ENSP00000377043.3	Q8N841-1
	TTLL6	ENST00000433608.6	TSL:1	c.*1-206A>G		intron	N/A	ENSP00000399211.2	A0AAA9X7X9
	TTLL6	ENST00000376681.7	TSL:1	n.*2084-206A>G		intron	N/A	ENSP00000365871.4	F8WDP8

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		0.83

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: rs7219021; hg19: chr17-46840541;