rs1555907480

Positions:

• chr22-50221068-C-A
• chr22-50221068-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The ENST00000248846.10(TUBGCP6):​c.3291G>T​(p.Val1097=) 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. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. V1097V) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 34)
• Consequence: TUBGCP6 ENST00000248846.10 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.24

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 -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP6: Variant 22-50221068-C-A is Benign according to our data. Variant chr22-50221068-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 437151.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.24 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBGCP6	NM_020461.4	c.3291G>T	p.Val1097=	synonymous_variant	16/25	ENST00000248846.10	NP_065194.3
TUBGCP6	XR_001755343.3	n.3855G>T		non_coding_transcript_exon_variant	16/20
TUBGCP6	XR_938347.3	n.3855G>T		non_coding_transcript_exon_variant	16/23
TUBGCP6	XR_007067982.1	n.3048+960G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUBGCP6	ENST00000248846.10	c.3291G>T	p.Val1097=	synonymous_variant	16/25	1	NM_020461.4	ENSP00000248846	P1
TUBGCP6	ENST00000439308.6	c.3291G>T	p.Val1097=	synonymous_variant	16/25	1		ENSP00000397387
TUBGCP6	ENST00000498611.5	n.3617+207G>T		intron_variant, non_coding_transcript_variant		1
TUBGCP6	ENST00000491449.5	n.1598G>T		non_coding_transcript_exon_variant	8/16	5

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 34

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

Sep 22, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.89
DANN	Benign	0.57

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: rs1555907480; hg19: chr22-50659497;