chr22-50223440-T-C

Position:

• chr22-50223440-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.2270+701A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,634 control chromosomes in the GnomAD database, including 49,823 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 0.80 (49691 hom., cov: 33)
  • Exomes 𝑓: 0.74 (132 hom.)
• Consequence: TUBGCP6 NM_020461.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBGCP6	NM_020461.4	c.2270+701A>G		intron_variant		ENST00000248846.10	NP_065194.3
TUBGCP6	XR_001755343.3	n.2834+701A>G		intron_variant
TUBGCP6	XR_007067982.1	n.2834+701A>G		intron_variant
TUBGCP6	XR_938347.3	n.2834+701A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUBGCP6	ENST00000248846.10	c.2270+701A>G		intron_variant		1	NM_020461.4	ENSP00000248846.5

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121952 AN: 152052 Hom.: 49640 Cov.: 33

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.776

GnomAD4 exome AF: 0.737 AC: 342 AN: 464 Hom.: 132 Cov.: 0 AF XY: 0.765 AC XY: 208 AN XY: 272

Gnomad4 AMR exome AF: 0.571

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.833

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.700

Gnomad4 NFE exome AF: 0.739

Gnomad4 OTH exome AF: 0.792

GnomAD4 genome AF: 0.802 AC: 122052 AN: 152170 Hom.: 49691 Cov.: 33 AF XY: 0.806 AC XY: 59947 AN XY: 74384

Gnomad4 AFR AF: 0.947

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.772

Alfa AF: 0.754 Hom.: 16677

Bravo AF: 0.798

Asia WGS AF: 0.834 AC: 2899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.34

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: rs5771242; hg19: chr22-50661869;