ENST00000450755.1:n.486G>A

Variant names:

• chrX-123562127-G-A
• rs72631819
• ENST00000450755.1:n.486G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.09
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TUBB4AP1		n.123562127G>A		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00726 AC: 811 AN: 111781 Hom.: 0 Cov.: 22

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

GnomAD2 exomes AF: 0.00741 AC: 1360 AN: 183437 AF XY: 0.00803

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 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.: 59 Cov.: 28 AF XY: 0.00999 AC XY: 3249 AN XY: 325223

African (AFR) AF: 0.00165 AC: 41 AN: 24794

American (AMR) AF: 0.00644 AC: 225 AN: 34924

Ashkenazi Jewish (ASJ) AF: 0.00170 AC: 32 AN: 18867

East Asian (EAS) AF: 0.0000672 AC: 2 AN: 29761

South Asian (SAS) AF: 0.00611 AC: 321 AN: 52494

European-Finnish (FIN) AF: 0.00252 AC: 101 AN: 40060

Middle Eastern (MID) AF: 0.00303 AC: 12 AN: 3959

European-Non Finnish (NFE) AF: 0.0124 AC: 9531 AN: 771489

Other (OTH) AF: 0.00926 AC: 401 AN: 43299

GnomAD4 genome AF: 0.00724 AC: 810 AN: 111833 Hom.: 0 Cov.: 22 AF XY: 0.00644 AC XY: 219 AN XY: 33997

African (AFR) AF: 0.00198 AC: 61 AN: 30772

American (AMR) AF: 0.0101 AC: 107 AN: 10612

Ashkenazi Jewish (ASJ) AF: 0.00226 AC: 6 AN: 2652

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

South Asian (SAS) AF: 0.00527 AC: 14 AN: 2656

European-Finnish (FIN) AF: 0.00247 AC: 15 AN: 6079

Middle Eastern (MID) AF: 0.0139 AC: 3 AN: 216

European-Non Finnish (NFE) AF: 0.0111 AC: 591 AN: 53103

Other (OTH) AF: 0.00784 AC: 12 AN: 1531

Alfa AF: 0.00753 Hom.: 57

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
PhyloP100		4.1

Splicing

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

Other links and lift over

dbSNP: rs72631819; hg19: chrX-122695978;