X-123562163-A-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUBB4AP1		n.123562163A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUBB4AP1	ENST00000450755.1	n.522A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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

Other links and lift over

dbSNP: rs72631817; hg19: chrX-122696014;