Genetic Variant TUBB4AP1:n.486G>C (chrX-123562127-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000450755.1(TUBB4AP1):n.486G>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.00000098 in 1,019,957 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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: 22)

Exomes 𝑓: 9.8e-7 ( 0 hom. 0 hem. )

Consequence

TUBB4AP1
ENST00000450755.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.09

Publications

0 publications found

Variant links:

Genes affected

TUBB4AP1 (HGNC:42340): (tubulin beta 4A class IVa pseudogene 1)

TUBB4AP1 links:

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ACMG classification

Classification was made for transcript

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=-0.71).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUBB4AP1		n.123562127G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUBB4AP1	ENST00000450755.1 link	n.486G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

9.80e-7

AC:

AN:

1019957

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

325235

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24794

American (AMR)

AF:

0.00

AC:

AN:

34924

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18869

East Asian (EAS)

AF:

0.00

AC:

AN:

29763

South Asian (SAS)

AF:

0.00

AC:

AN:

52498

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40062

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3959

European-Non Finnish (NFE)

AF:

0.00000130

AC:

AN:

771782

Other (OTH)

AF:

0.00

AC:

AN:

43306

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

7.9

(source)

DANN

Benign

0.29

PhyloP100

4.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over