rs1296279

Positions:

• chr17-59888370-G-A
• chr17-59888370-G-T

Variant summary

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

The NM_016261.4(TUBD1):​c.173-2140C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,114 control chromosomes in the GnomAD database, including 2,469 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 0.17 (2469 hom., cov: 32)
• Consequence: TUBD1 NM_016261.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUBD1	NM_016261.4	c.173-2140C>T		intron_variant		ENST00000325752.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUBD1	ENST00000325752.8	c.173-2140C>T		intron_variant		5	NM_016261.4	P1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25493 AN: 151996 Hom.: 2460 Cov.: 32

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.168

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.168 AC: 25518 AN: 152114 Hom.: 2469 Cov.: 32 AF XY: 0.169 AC XY: 12553 AN XY: 74358

Gnomad4 AFR AF: 0.0955

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.178

Alfa AF: 0.174 Hom.: 399

Bravo AF: 0.159

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.8
DANN	Benign	0.58

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: rs1296279; hg19: chr17-57965731;