rs778386409

chr22-50221059-A-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_020461.4(TUBGCP6):c.3300T>C(p.Thr1100=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00098 (0 hom., cov: 31)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TUBGCP6 NM_020461.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.68

Genes affected

TUBGCP6 (HGNC:18127): (tubulin gamma complex component 6) The protein encoded by this gene is part of a large multisubunit complex required for microtubule nucleation at the centrosome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 22-50221059-A-G is Benign according to our data. Variant chr22-50221059-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 437150.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUBGCP6	NM_020461.4	c.3300T>C	p.Thr1100=	synonymous_variant	16/25	ENST00000248846.10
TUBGCP6	XR_001755343.3	n.3864T>C		non_coding_transcript_exon_variant	16/20
TUBGCP6	XR_938347.3	n.3864T>C		non_coding_transcript_exon_variant	16/23
TUBGCP6	XR_007067982.1	n.3048+969T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUBGCP6	ENST00000248846.10	c.3300T>C	p.Thr1100=	synonymous_variant	16/25	1	NM_020461.4	P1
TUBGCP6	ENST00000439308.6	c.3300T>C	p.Thr1100=	synonymous_variant	16/25	1
TUBGCP6	ENST00000498611.5	n.3617+216T>C		intron_variant, non_coding_transcript_variant		1
TUBGCP6	ENST00000491449.5	n.1607T>C		non_coding_transcript_exon_variant	8/16	5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 89 AN: 91700 Hom.: 0 Cov.: 31 FAILED QC

Gnomad AFR AF: 0.00144

Gnomad AMI AF: 0.00218

Gnomad AMR AF: 0.000933

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.00185

Gnomad FIN AF: 0.000380

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000709

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 7.07e-7 AC: 1 AN: 1414462 Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0 AN XY: 704286

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000237

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000980 AC: 90 AN: 91794 Hom.: 0 Cov.: 31 AF XY: 0.000744 AC XY: 33 AN XY: 44342

Gnomad4 AFR AF: 0.00147

Gnomad4 AMR AF: 0.000931

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.00185

Gnomad4 FIN AF: 0.000380

Gnomad4 NFE AF: 0.000709

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0862 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Mar 01, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.90
Dann	Benign	0.40

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: rs778386409; hg19: chr22-50659488; COSMIC: COSV50536223; COSMIC: COSV50536223;