chr22-43166823-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015140.4(TTLL12):​c.*1185C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 176,574 control chromosomes in the GnomAD database, including 12,756 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 0.37 ( 10889 hom., cov: 33)
Exomes 𝑓: 0.36 ( 1867 hom. )

Consequence

TTLL12
NM_015140.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.364
Variant links:
Genes affected
TTLL12 (HGNC:28974): (tubulin tyrosine ligase like 12) Enables H4K20me3 modified histone binding activity and tubulin binding activity. Involved in negative regulation of type I interferon-mediated signaling pathway and regulation of mitotic cell cycle. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TTLL12NM_015140.4 linkuse as main transcriptc.*1185C>A 3_prime_UTR_variant 14/14 ENST00000216129.7 NP_055955.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TTLL12ENST00000216129.7 linkuse as main transcriptc.*1185C>A 3_prime_UTR_variant 14/141 NM_015140.4 ENSP00000216129 P1
TTLL12ENST00000484711.1 linkuse as main transcriptn.2251C>A non_coding_transcript_exon_variant 3/32

Frequencies

GnomAD3 genomes
AF:
0.370
AC:
56162
AN:
151982
Hom.:
10879
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.349
Gnomad AMI
AF:
0.385
Gnomad AMR
AF:
0.408
Gnomad ASJ
AF:
0.424
Gnomad EAS
AF:
0.00656
Gnomad SAS
AF:
0.268
Gnomad FIN
AF:
0.347
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.407
Gnomad OTH
AF:
0.395
GnomAD4 exome
AF:
0.362
AC:
8858
AN:
24474
Hom.:
1867
Cov.:
0
AF XY:
0.349
AC XY:
4616
AN XY:
13220
show subpopulations
Gnomad4 AFR exome
AF:
0.319
Gnomad4 AMR exome
AF:
0.373
Gnomad4 ASJ exome
AF:
0.408
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.285
Gnomad4 FIN exome
AF:
0.361
Gnomad4 NFE exome
AF:
0.403
Gnomad4 OTH exome
AF:
0.371
GnomAD4 genome
AF:
0.370
AC:
56204
AN:
152100
Hom.:
10889
Cov.:
33
AF XY:
0.364
AC XY:
27094
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.349
Gnomad4 AMR
AF:
0.409
Gnomad4 ASJ
AF:
0.424
Gnomad4 EAS
AF:
0.00677
Gnomad4 SAS
AF:
0.271
Gnomad4 FIN
AF:
0.347
Gnomad4 NFE
AF:
0.407
Gnomad4 OTH
AF:
0.389
Alfa
AF:
0.392
Hom.:
14585
Bravo
AF:
0.373
Asia WGS
AF:
0.155
AC:
542
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.36
DANN
Benign
0.59
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs47340; hg19: chr22-43562829; API