rs72631817

Positions:

• chrX-123562163-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000450755.1(TUBB4AP1):​n.522A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.00746 in 1,092,831 control chromosomes in the GnomAD database, including 351 homozygotes. There are 2,153 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 0.036 (180 hom., 1108 hem., cov: 22)
  • Exomes 𝑓: 0.0042 (171 hom. 1045 hem.)
• Consequence: TUBB4AP1 ENST00000450755.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.12

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBB4AP1		n.123562163A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUBB4AP1	ENST00000450755.1	n.522A>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.0364 AC: 4062 AN: 111664 Hom.: 180 Cov.: 22 AF XY: 0.0325 AC XY: 1102 AN XY: 33894

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0141

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00151

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0126

Gnomad NFE AF: 0.000490

Gnomad OTH AF: 0.0378

GnomAD3 exomes AF: 0.0105 AC: 1935 AN: 183483 Hom.: 76 AF XY: 0.00695 AC XY: 472 AN XY: 67917

Gnomad AFR exome AF: 0.132

Gnomad AMR exome AF: 0.00540

Gnomad ASJ exome AF: 0.000134

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000314

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000268

Gnomad OTH exome AF: 0.00486

GnomAD4 exome AF: 0.00417 AC: 4091 AN: 981113 Hom.: 171 Cov.: 27 AF XY: 0.00337 AC XY: 1045 AN XY: 310111

Gnomad4 AFR exome AF: 0.134

Gnomad4 AMR exome AF: 0.00657

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000618

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000231

Gnomad4 OTH exome AF: 0.0107

GnomAD4 genome AF: 0.0364 AC: 4065 AN: 111718 Hom.: 180 Cov.: 22 AF XY: 0.0326 AC XY: 1108 AN XY: 33958

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0141

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00151

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000490

Gnomad4 OTH AF: 0.0373

Alfa AF: 0.0189 Hom.: 100

Bravo AF: 0.0426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72631817; hg19: chrX-122696014;