Genetic Variant NM_024686.6:c.1143-1041C>G (chr1-83922435-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024686.6(TTLL7):c.1143-1041C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,904 control chromosomes in the GnomAD database, including 19,224 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 0.49 ( 19224 hom., cov: 31)

Consequence

TTLL7
NM_024686.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.548

Publications

3 publications found

Variant links:

Genes affected

TTLL7 (HGNC:26242): (tubulin tyrosine ligase like 7) Enables alpha-tubulin binding activity; beta-tubulin binding activity; and tubulin-glutamic acid ligase activity. Involved in protein polyglutamylation. Predicted to be located in 9+0 non-motile cilium and ciliary basal body. Predicted to be active in cilium. [provided by Alliance of Genome Resources, Apr 2022]

TTLL7 links:

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new If you want to explore the variant's impact on the transcript NM_024686.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024686.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TTLL7	NM_024686.6	MANE Select	c.1143-1041C>G	intron	N/A	NP_078962.4
TTLL7	NM_001350214.2		c.1143-1041C>G	intron	N/A	NP_001337143.1	Q6ZT98-1
TTLL7	NM_001350215.2		c.1062-1041C>G	intron	N/A	NP_001337144.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TTLL7	ENST00000260505.13	TSL:2 MANE Select	c.1143-1041C>G	intron	N/A	ENSP00000260505.8	Q6ZT98-1
TTLL7	ENST00000474957.5	TSL:1	n.198-1041C>G	intron	N/A	ENSP00000434146.1	F2Z2J7
TTLL7	ENST00000477524.5	TSL:1	n.1481-1041C>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.494

AC:

74955

AN:

151786

Hom.:

19219

Cov.:

show subpopulations

Gnomad AFR

AF:

0.371

Gnomad AMI

AF:

0.478

Gnomad AMR

AF:

0.540

Gnomad ASJ

AF:

0.530

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.376

Gnomad FIN

AF:

0.560

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.570

Gnomad OTH

AF:

0.500

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

GnomAD4 genome

AF:

0.494

AC:

74978

AN:

151904

Hom.:

19224

Cov.:

AF XY:

0.489

AC XY:

36286

AN XY:

74220

show subpopulations

African (AFR)

AF:

0.371

AC:

15379

AN:

41440

American (AMR)

AF:

0.540

AC:

8230

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.530

AC:

1836

AN:

3464

East Asian (EAS)

AF:

0.286

AC:

1474

AN:

5152

South Asian (SAS)

AF:

0.375

AC:

1806

AN:

4810

European-Finnish (FIN)

AF:

0.560

AC:

5918

AN:

10562

Middle Eastern (MID)

AF:

0.422

AC:

124

AN:

294

European-Non Finnish (NFE)

AF:

0.570

AC:

38732

AN:

67920

Other (OTH)

AF:

0.495

AC:

1043

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1899

3798

5698

7597

9496

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

670

1340

2010

2680

3350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.387

Hom.:

1042

Bravo

AF:

0.494

Asia WGS

AF:

0.344

AC:

1195

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.4

(source)

DANN

Benign

0.49

PhyloP100

-0.55

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over