rs141805017

Positions:

• chr22-50233406-C-A
• chr22-50233406-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_020461.4(TUBGCP6):​c.1026G>T​(p.Pro342Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: TUBGCP6 NM_020461.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.22

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]

TUBGCP6 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP7: Synonymous conserved (PhyloP=-4.22 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBGCP6	NM_020461.4	c.1026G>T	p.Pro342Pro	synonymous_variant	3/25	ENST00000248846.10	NP_065194.3
TUBGCP6	XR_001755343.3	n.1590G>T		non_coding_transcript_exon_variant	3/20
TUBGCP6	XR_007067982.1	n.1590G>T		non_coding_transcript_exon_variant	3/19
TUBGCP6	XR_938347.3	n.1590G>T		non_coding_transcript_exon_variant	3/23

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUBGCP6	ENST00000248846.10	c.1026G>T	p.Pro342Pro	synonymous_variant	3/25	1	NM_020461.4	ENSP00000248846.5
TUBGCP6	ENST00000439308.6	c.1026G>T	p.Pro342Pro	synonymous_variant	3/25	1		ENSP00000397387.2
TUBGCP6	ENST00000498611.5	n.1559G>T		non_coding_transcript_exon_variant	3/23	1
TUBGCP6	ENST00000434349.1	c.255G>T	p.Pro85Pro	synonymous_variant	2/6	5		ENSP00000409650.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	0.10
DANN	Benign	0.72

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: rs141805017; hg19: chr22-50671835;