rs72631819

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chrX-123562127-G-A
• chrX-123562127-G-C
• chrX-123562127-G-T

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

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.486G>A		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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;