chr17-59869851-T-C

Variant names:

• chr17-59869851-T-C
• rs1292045
• NM_016261.4:c.935-3102A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TUBD1	NM_016261.4	c.935-3102A>G		intron_variant	Intron 6 of 8	ENST00000325752.8	NP_057345.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUBD1	ENST00000325752.8	c.935-3102A>G		intron_variant	Intron 6 of 8	5	NM_016261.4	ENSP00000320797.3

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

African (AFR) AF: 0.668 AC: 27686 AN: 41420

American (AMR) AF: 0.527 AC: 8024 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1476 AN: 3468

East Asian (EAS) AF: 0.560 AC: 2890 AN: 5160

South Asian (SAS) AF: 0.433 AC: 2081 AN: 4810

European-Finnish (FIN) AF: 0.446 AC: 4694 AN: 10518

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32500 AN: 67946

Other (OTH) AF: 0.552 AC: 1164 AN: 2108

Alfa AF: 0.496 Hom.: 24348

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
PhyloP100		-3.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1292045; hg19: chr17-57947212;