rs7511006

chr22-50237830-T-C

Variant summary

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

The NM_020461.4(TUBGCP6):c.905+2374A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,092 control chromosomes in the GnomAD database, including 8,239 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 0.31 (8239 hom., cov: 33)
• Consequence: TUBGCP6 NM_020461.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUBGCP6	NM_020461.4	c.905+2374A>G		intron_variant		ENST00000248846.10
TUBGCP6	XR_001755343.3	n.1469+2374A>G		intron_variant, non_coding_transcript_variant
TUBGCP6	XR_007067982.1	n.1469+2374A>G		intron_variant, non_coding_transcript_variant
TUBGCP6	XR_938347.3	n.1469+2374A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUBGCP6	ENST00000248846.10	c.905+2374A>G		intron_variant		1	NM_020461.4	P1
TUBGCP6	ENST00000439308.6	c.905+2374A>G		intron_variant		1
TUBGCP6	ENST00000498611.5	n.1438+2374A>G		intron_variant, non_coding_transcript_variant		1
TUBGCP6	ENST00000434349.1	c.136+2395A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46985 AN: 151974 Hom.: 8241 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.309 AC: 46978 AN: 152092 Hom.: 8239 Cov.: 33 AF XY: 0.308 AC XY: 22941 AN XY: 74368

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.298

Alfa AF: 0.347 Hom.: 3042

Bravo AF: 0.291

Asia WGS AF: 0.304 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.4
Dann	Benign	0.52

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: rs7511006; hg19: chr22-50676259;