17-59869851-T-C

Position:

• chr17-59869851-T-C

Variant summary

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

The NM_016261.4(TUBD1):​c.935-3102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,848 control chromosomes in the GnomAD database, including 22,381 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 0.53 (22381 hom., cov: 31)
• Consequence: TUBD1 NM_016261.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.86

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBD1	NM_016261.4	c.935-3102A>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.935-3102A>G		intron_variant		5	NM_016261.4	ENSP00000320797	P1

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81121 AN: 151730 Hom.: 22352 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.535 AC: 81205 AN: 151848 Hom.: 22381 Cov.: 31 AF XY: 0.532 AC XY: 39507 AN XY: 74194

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.552

Alfa AF: 0.489 Hom.: 18042

Bravo AF: 0.545

Asia WGS AF: 0.562 AC: 1957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.025
DANN	Benign	0.55

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: rs1292045; hg19: chr17-57947212;