rs72631817

Variant names:

• chrX-123562163-A-G
• rs72631817
• ENST00000450755.1:n.522A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450755.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TUBB4AP1	ENST00000450755.1	TSL:6	n.522A>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0364 AC: 4062 AN: 111664 Hom.: 180 Cov.: 22

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

GnomAD2 exomes AF: 0.0105 AC: 1935 AN: 183483 AF XY: 0.00695

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 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

African (AFR) AF: 0.134 AC: 3191 AN: 23898

American (AMR) AF: 0.00657 AC: 229 AN: 34877

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18602

East Asian (EAS) AF: 0.00 AC: 0 AN: 29532

South Asian (SAS) AF: 0.000618 AC: 32 AN: 51740

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40006

Middle Eastern (MID) AF: 0.00564 AC: 22 AN: 3904

European-Non Finnish (NFE) AF: 0.000231 AC: 170 AN: 736585

Other (OTH) AF: 0.0107 AC: 447 AN: 41969

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

African (AFR) AF: 0.125 AC: 3826 AN: 30650

American (AMR) AF: 0.0141 AC: 150 AN: 10639

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2648

East Asian (EAS) AF: 0.00 AC: 0 AN: 3528

South Asian (SAS) AF: 0.00151 AC: 4 AN: 2649

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6082

Middle Eastern (MID) AF: 0.00917 AC: 2 AN: 218

European-Non Finnish (NFE) AF: 0.000490 AC: 26 AN: 53091

Other (OTH) AF: 0.0373 AC: 57 AN: 1528

Alfa AF: 0.0189 Hom.: 100

Bravo AF: 0.0426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.67
PhyloP100		6.1

Splicing

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.

Other links and lift over

dbSNP: rs72631817;

hg19: chrX-122696014;