rs12150500

Positions:

• chr17-59878393-G-C

Variant summary

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

The NM_016261.4(TUBD1):​c.538-59C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,229,726 control chromosomes in the GnomAD database, including 14,614 homozygotes. 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 0.14 (1690 hom., cov: 31)
  • Exomes 𝑓: 0.15 (12924 hom.)
• Consequence: TUBD1 NM_016261.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

Genes affected

TUBD1 (HGNC:16811): (tubulin delta 1) Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization; mitotic cell cycle; and positive regulation of smoothened signaling pathway. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBD1	NM_016261.4	c.538-59C>G		intron_variant		ENST00000325752.8	NP_057345.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUBD1	ENST00000325752.8	c.538-59C>G		intron_variant		5	NM_016261.4	ENSP00000320797	P1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21605 AN: 151820 Hom.: 1692 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0528

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.153

GnomAD4 exome AF: 0.152 AC: 163980 AN: 1077798 Hom.: 12924 Cov.: 14 AF XY: 0.151 AC XY: 82450 AN XY: 546588

Gnomad4 AFR exome AF: 0.105

Gnomad4 AMR exome AF: 0.149

Gnomad4 ASJ exome AF: 0.163

Gnomad4 EAS exome AF: 0.0334

Gnomad4 SAS exome AF: 0.111

Gnomad4 FIN exome AF: 0.157

Gnomad4 NFE exome AF: 0.163

Gnomad4 OTH exome AF: 0.149

GnomAD4 genome AF: 0.142 AC: 21595 AN: 151928 Hom.: 1690 Cov.: 31 AF XY: 0.142 AC XY: 10564 AN XY: 74254

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0528

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.151

Alfa AF: 0.152 Hom.: 228

Bravo AF: 0.141

Asia WGS AF: 0.0790 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12150500; hg19: chr17-57955754;