Variant rs72631819 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000450755.1(TUBB4AP1):n.486G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0101 in 1,131,480 control chromosomes in the GnomAD database, including 59 homozygotes. There are 3,468 hemizygotes 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: 𝑓 0.0072 ( 0 hom., 219 hem., cov: 22)

Exomes 𝑓: 0.010 ( 59 hom. 3249 hem. )

Consequence

TUBB4AP1
ENST00000450755.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.09

Variant links:

Genes affected

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

TUBB4AP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BS2

High Hemizygotes in GnomAd4 at 219 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUBB4AP1	ENST00000450755.1 linkuse as main transcript	n.486G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.00726

AC:

811

AN:

111781

Hom.:

Cov.:

AF XY:

0.00645

AC XY:

219

AN XY:

33935

show subpopulations

Gnomad AFR

AF:

0.00199

Gnomad AMI

AF:

0.00146

Gnomad AMR

AF:

0.0101

Gnomad ASJ

AF:

0.00226

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00526

Gnomad FIN

AF:

0.00247

Gnomad MID

AF:

0.0169

Gnomad NFE

AF:

0.0111

Gnomad OTH

AF:

0.00794

GnomAD3 exomes

AF:

0.00741

AC:

1360

AN:

183437

Hom.:

AF XY:

0.00803

AC XY:

545

AN XY:

67869

show subpopulations

Gnomad AFR exome

AF:

0.00160

Gnomad AMR exome

AF:

0.00576

Gnomad ASJ exome

AF:

0.00214

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00645

Gnomad FIN exome

AF:

0.00281

Gnomad NFE exome

AF:

0.0117

Gnomad OTH exome

AF:

0.00839

GnomAD4 exome

AF:

0.0105

AC:

10666

AN:

1019647

Hom.:

Cov.:

AF XY:

0.00999

AC XY:

3249

AN XY:

325223

show subpopulations

Gnomad4 AFR exome

AF:

0.00165

Gnomad4 AMR exome

AF:

0.00644

Gnomad4 ASJ exome

AF:

0.00170

Gnomad4 EAS exome

AF:

0.0000672

Gnomad4 SAS exome

AF:

0.00611

Gnomad4 FIN exome

AF:

0.00252

Gnomad4 NFE exome

AF:

0.0124

Gnomad4 OTH exome

AF:

0.00926

GnomAD4 genome

AF:

0.00724

AC:

810

AN:

111833

Hom.:

Cov.:

AF XY:

0.00644

AC XY:

219

AN XY:

33997

show subpopulations

Gnomad4 AFR

AF:

0.00198

Gnomad4 AMR

AF:

0.0101

Gnomad4 ASJ

AF:

0.00226

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00527

Gnomad4 FIN

AF:

0.00247

Gnomad4 NFE

AF:

0.0111

Gnomad4 OTH

AF:

0.00784

Alfa

AF:

0.00753

Hom.:

Bravo

AF:

0.00743

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

8.1

DANN

Benign

0.72

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over